Thermodynamic model for the stabilization of trigonal thiolato mercury(II) in designed three-stranded coiled coils

A thermodynamic model is presented that describes the binding of Hg(II) to de novo designed peptides, Tri L9C and Baby L9C, which were derived from the Tri family. The Tri peptides are based on the parent sequence Ac-NH-G(LKALEEK)(x)()G-CONH(2) and are known to form two-stranded coiled coils at low pH (pH <4) and three-stranded coiled coils at high pH (pH >7). Tri L9C (x = 4) contains a four heptad repeat sequence with cysteine in position 9 and leucines in the other a and d positions; Baby L9C (x = 3), which also has a cysteine in position 9 but is one heptad shorter than Tri L9C, was designed to form less stable helical coiled coils in solution. The free energies of coiled coil formation for Tri, Tri L9C, Baby Tri, and Baby L9C at pH 2.5 and 8.5 were determined by guanidinium denaturation titrations; Tri L9C was observed to be highly helical in the absence of denaturant at pH 8.5 while Baby L9C contained <20% helical content at pH 8.5, indicating a weakly associated or unassociated coiled coil. Size-exclusion chromatography (SEC) verified that Baby L9C was a monomer at pH 8.5. The helicity of Baby L9C was induced by addition of HgCl(2). The subsequent formation of a trigonal thiolato Hg(II) in the interior of a three-stranded coiled coil was verified by the presence of a characteristic HgS(3) UV band at 248 nm. Titrations of Tri L9C and Baby L9C into solutions of HgCl(2) at pH values between 7 and 9 were performed to extract binding constants. Global fits to the data employed a mechanism that involved initial binding of mercury to the peptides forming a two-stranded coiled coil with linear thiolato Hg(II) at [peptide]/[Hg] <2, followed by addition of a more weakly associated third helix to generate a three-stranded coiled coil. This mechanism would require the deprotonation of the third cysteine thiol to generate the trigonal thiolato Hg(II) at pH >7.5 [the pK(a) of the cysteine thiol in the presence of Hg(II)]. Support for this mechanism was given by the observation of a three-stranded coiled coil by SEC in a solution of Tri L9C at pH 7.0.

Redox pathways in DNA oxidation: kinetic studies of guanine and sugar oxidation by para-substituted derivatives of oxoruthenium(IV)

The oxidation of nucleotides and DNA by a series of complexes based on Ru(tpy)(bpy)O2+ (1) was investigated (tpy = 2,2':6',2"-terpyridine; bpy = 2,2'-bipyridine). These complexes were substituted with electron-donating or-withdrawing substituents in the para positions of the polypyridyl ligands so that the oxidation potentials of the complexes were affected but the reaction trajectory of the oxo ligand with DNA was the same throughout the series. The prepared complexes were (with E1/2(III/II) and E1/2(IV/III) values in volts versus Ag/AgCl) Ru(4'-EtO-tpy)(bpy)O2+ (2; 0.47, 0.60), Ru(4'-Cl-tpy)(bpy)O2+ (3; 0.55, 0.63), Ru(tpy)(4,4'-Me2-bpy)O2+ (4; 0.48, 0.62), and Ru(tpy)(4,4'-Cl2-bpy)O2+ (5; 0.58, 0.63). The complexes oxidized deoxycytosine 5'-monophosphate at the sugar moiety (k = 0.24-0.47 M-1 s-1) and guanosine 5'-monophosphate at the base moiety (k = 6.1-15 M-1 s-1). The rate constants increase across these ranges in the order 3 > 1 > 4 > 2, which is the same order as the redox potentials of the complexes. The effect of the base on these reactions was also studied, and xanthine was found to react with 1 much faster than guanine while hypoxanthine was less reactive than the sugar moiety. The complexes all oxidized oligonucleotides to generate base-labile lesions at guanine and a combination of spontaneous and base-labile scission at the sugar functionalities. The selectivity of cleavage in duplex and single-stranded DNA was not a strong function of the substituents on the metal complex.