Introduction
The reaction of hydrogen peroxide with ferric porphyrins is of interest in relation to several classes of natural enzymes that use that metalloporphyrin as an essential cofactor. For instance, peroxidases catalyze the oxidation of a variety of substrates by hydrogen peroxide, whereas, catalases are enzymes that promote the disproportionation of hydrogen peroxide to give oxygen and water. Both classes of enzymes are highly efficient catalysts in which the formation of an outersphere porphyrin--hydrogen peroxide complex is generally the rate-determining step (1). Horseradish peroxidase (HRP), the most thoroughly studied and representative peroxidase enzyme, reacts with hydrogen peroxide, hydroperoxides, or peracids to form two distinct intermediates known as compounds I and II (2). Compound I is a green species (3) possessing two oxidizing equivalents above the Fe(III) state, and a variety of spectroscopic and kinetic studies have indicated that it is an oxo-ligated Fe(IV) porphyrin radical cation ([Fe.sup.IV]O[P.sup.+.]) (4-9). Compound II is also a Fe(IV) species ([Fe.sup.IV]OP), but possesses one fewer oxidizing equivalent (4-9). Extensive studies have established that the peroxidation reaction catalyzed by HRP (and other peroxidases) proceeds according to the enzymatic cycle shown in Scheme 1 (4-9), where A[H.sub.2], a reducing substrate, is converted into a free radical species (A[H.sup..]) by one-electron oxidation processes. A key mechanistic question concerning peroxidase catalysis is the means by which the high reaction rates for the generation of compound I are achieved. In this respect, a number of studies with peroxidase model systems have been carried out. For example, a series of articles from Traylor and coworkers (10-12) detail the oxidation reactions promoted by several ferric protoporphyrin derivatives, in methanol as solvent, using either hydrogen peroxide or a peracid as the oxidant. In comparison to hemin itself, it was reported that all derivatives possessing a covalently attached base were catalytically more active, and the observed rate accelerations upon attachment of a basic functionality were attributed to either a "proximal base effect", an intramolecular bonding interaction between the hemin and the base, or a "distal base effect", intramolecular general catalysis. Also of note, the addition of nitrogenous bases to the medium increased the reaction rate, an effect that presumably arises from intermolecular general catalysis. Other model studies on nonaggregating, water-soluble iron(III) porphyrins, which possessed meso-phenyl rings, yielded evidence for the occurrence of general catalysis by nitrogenous buffers, including 2,4,6-collidine (13).
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In line with these studies on peroxidase model systems, a guanine-rich DNA oligomer and its corresponding RNA version ("PS2.M" and "rPS2.M", respectively) were found to bind hemin (1) with dissociation constants of 27 [+ or -] 2 nmol/L and 0.9 [+ or -] 0.2 [micro]mol/L, respectively (14). Remarkably, PS2.M-hemin and rPS2.M-hemin complexes were found to possess high peroxidation activity, despite PS2.M being selected from a random sequence single-stranded DNA library for the specific binding of a different porphyrin, N-methyl mesoporphyrin IX (NMM, 2) (14, 15).
The PS2.M-hemin and rPS2.M-hemin complexes could therefore be regarded as a new category of deoxyribozyme (DNAzyme) and ribozyme, respectively. Recently, they have found practical applications (16, 17). UV-vis and electron paramagnetic resonance (EPR) spectroscopies (14, 18) indicated that the hemin iron changed the character of its coordination upon complexation to the folded nucleic acid oligomers. Thus, the observed spectra more closely resemble those of horseradish peroxidase (HRP) and other hemoproteins rather than those associated with uncomplexed hemin.
We have recently reported a pair of models for the actively folded structure of PS2.M and these two structures are shown in Fig. 1 (19). Two loop …
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