Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT).

A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major groove by Hoogsteen hydrogen bonds. This structure provides a basis for comparison with triplexes containing noncanonical or nonnatural nucleotides.

Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand.

Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-PCPCPCPP) (PDD-EG), which contains 5-(1-propynl)-2'-deoxyuridine (P) in the third strand and hexakis(ethylene glycol) linkers [(EG)6]. The structure was calculated using X-PLOR with distance and dihedral angle restraints obtained from two-dimensional NMR experiments and refined with the direct relaxation matrix method. The structures show that the extended aromatic electron cloud of the propynylU nucleotide stacks well over the 5'-neighboring nucleotides, resulting in increased stabilization. The propynylU nucleotides also affect the overall structure of the triple helix. A comparison of the structure to that of the nonmodified intramolecular DNA triplex of the same sequence, d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT) (DDD-EG), shows that PDD-EG has a more A-DNA like X displacement and inclination than DDD-EG yet still maintains predominantly S-type sugar puckers as found in DDD-EG and other DNA triplexes.

Quantitating direct chlorine transfer from enzyme to substrate in chloroperoxidase-catalyzed reactions.

Substrate competition methods that were previously used to quantitate the involvement of free Cl2 in the chloride-dependent peroxidatic reactions catalyzed by chloroperoxidase (CPO) (Libby, R. D., Shedd, A. L., Phipps, K. A., Beachy, T. M., and Gerstberger, S. M., (1992) J. Biol. Chem. 267, 1769-1775) are extended to CPO-catalyzed halogenation reactions. Relative substrate specificities of halogen acceptor substrates (RHs) antipyrine (ap), NADH, 2-chlorodimedone (2cd), and barbituric acid (ba) are compared with previously studied peroxidatic substrates catechol (cat) and 2, 4,6-trimethylphenol (tmp) in their reactions with the CPO-H2O2-Cl system versus the hypochlorite-Cl system. Studies were carried out at pH 2.75 over a chloride concentration range of 1-100 mM and at pH 4.80 over a chloride concentration range of 100-400 mM. Competition studies involved successive pairwise comparisons of substrates of increasing enzyme specificity. The orders of specificities, ba > 2cd > ap > cat > tmp at pH 2.75 and ba > 2cd > NADH > ap > cat > tmp at pH 4.80, are the same for both the CPO-H2O2-Cl and hypochlorite-Cl systems. However, the magnitudes of the specificities are different between the two systems. In all comparisons except ap versus cat, the specificity of the CPO-H2O2-Cl system toward the preferred substrate is higher than that of the hypochlorite-Cl system. Quantitative comparisons between specificities of CPO-H2O2-Cl and hypochlorite-Cl systems indicate that at least 98% of the CPO-catalyzed halogenation reactions of ba, 2cd, NADH, and ap occur by mechanisms in which the substrate reacts directly with the enzyme. Thus, less than 2% of any of the CPO reactions could possibly involve a free oxidized halogen intermediate. All data are consistent with a mechanism in which RH binds to the CPO chlorinating intermediate (EOCl), and the chlorine atom is transferred directly from EOCl to RH. Further, the results indicate that any halogenation substrate with a higher CPO specificity than ap must also undergo direct chlorine transfer from the enzyme. These results underscore the critical need for quantitative kinetic evidence in establishing the extent of involvement of any potential reaction intermediate. Finally, this work calls into question the long held assumption of the obligatory involvement of hypochlorite as an intermediate in myeloperoxidase reactions. It supports the recent kinetic evidence presented by Marquet and Dunford for direct chlorine transfer in myeloperoxidase-catalyzed chlorination of tuarine (Marquet, L. A., and Dunford, H. B. (1994) J. Biol. Chem. 269, 7950-7956).

Defining the involvement of HOCl or Cl2 as enzyme-generated intermediates in chloroperoxidase-catalyzed reactions.

Peroxidatic substrates, catechol (CAT) and 2,4,6-trimethylphenol (TMP) were used as probes of thechloride dependent reactions catalyzed by chloroperoxidase (CPO). TMP is consumed only in the presence of chloride. TMP is a competitive inhibitor versus CAT, but CAT is a noncompetitive inhibitor versus TMP in chloride-dependent CPO-catalyzed peroxidation reactions. The ratio of TMP versus CAT consumed by the chloride-dependent CPO reaction in direct competition studies increases as the chloride concentration is increased from 1.0 to 400 mM. Ratios of non-enzymatic HOCl reactions under conditions otherwise similar to those of the CPO reactions are relatively insensitive to changes in chloride concentration and are experimentally indistinguishable from the values attained by the enzyme system at high chloride concentrations. Comparison of enzymatic ratios with those of the HOCl reactions indicate that the proportion of the enzymatic reaction involving a freely dissociable, enzyme-generated, oxidized halogen species varies from 10% at low chloride concentrations to essentially 100% at high chloride concentrations. All data are consistent with a mechanism in which chloride competes with CAT for binding to both CPO compound I and the CPO chlorinating intermediate (EOCl). Chloride binding to CPO compound I leads to the formation of EOCl and initiates the CPO chloride-dependent pathway. When CAT binds to either compound I or EOCl, it is directly oxidized to product. When chloride binds to EOCl, it either induces release of HOCl or reacts with EOCl to produce Cl2, which is released from the enzyme. TMP and CAT compete for reaction with the free oxidized halogen species. This is the first direct evidence for kinetically significant involvement of a free oxidized halogen species as an intermediate in any CPO-catalyzed reaction.