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The 3'-fluoromodified nucleotide analogs 3'-fluorothymidine triphosphate (FdTTP), 2',3'-dideoxy-3'-fluoro-5-chlorouridine triphosphate (F-5CldUTP), 2',3'-dideoxy-3'-fluoro-5-ethyluridine triphosphate (F-5EtdUTP), 2',3'-dideoxy-3'-fluorouridine triphosphate (FdUTP), and 2',3'-dideoxy-3'-fluoro-5-fluorouridine triphosphate (F-5FdUTP) as well as 2',3'-dideoxythymidine triphosphate (ddTTP), 2',3'-didehydro-2',3'-dideoxythymidine triphosphate (ddeTTP), 3'-chlorothymidine triphosphate (CldTTP), and 3'-rhodanothymidine triphosphate (SCNdTTP) were tested for their ability to inhibit hepatitis B virus (HBV)-associated DNA polymerase activity in vitro. The ID50 values of the most potent inhibitors were 0.15 microM for FdTTP, 0.2 microM for ddeTTP, 0.45 microM for ddTTP, and 0.8 microM for F-5CldUTP. SCNdTTP, CldTTP, and F-5EtdUTP were less efficient (ID50 = 3-5 microM), and FdUTP and F-5FdUTP were the least efficient inhibitors (ID50 = 25 microM) of the enzyme activity. Kinetic analysis revealed a competitive type of inhibition for FdTTP and ddeTTP. The Ki values were estimated to be 0.04 microM and 0.08 microM, respectively, compared with a Km value for dTTP of about 0.18 microM.

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Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to explore noncovalent interactions between different peptides and ribose nucleic acids (RNAs). One RNA was mixed together with two or more peptides or vice versa to compare the different effects of the molecules for noncovalent complex formation. The matrix 2,4,6-trihydroxyacetophenone was considered optimal for these studies due to the fact that peptides and RNA showed roughly the same peak intensities, in negative ion mode, as well as RNA-peptide complexes being detected. The formation of the noncovalent RNA-peptide complexes showed a correlation with the number of the basic amino acids arginine, lysine and histidine. The strongest influence of these amino acids for complex formation was obtained with arginine. Although different RNA molecules were used with different compositions and secondary structures, no specific effects to complex formation was observed. The comparison of noncovalent complexes with covalent RNA-peptide complexes, which were obtained from ribosomal subunits after cross-linking and enzymatic cleavages, showed that the specific RNA-protein interactions are dependent on the three-dimensional structure of the ribosome and its components. The results of this report indicate that MALDI-MS may be useful for the study of noncovalent interactions, in particular for peptides and RNA.