Ribozymes, metal activation

Insofar metal activities are required for both inheritance and ribozyme functions, and RNA will enrich but Zn and Mg upon its formation (which apparently is not a conceivable part of chemical - rather than biological - evolution), this provides an additional argument against any kind of RNA-world which would rely upon no additional kinds of polymers. Instead, peptides or even proteins would be required to provide the very... 

The hypothesis that our biological world built on the DNA-RNA-protein central dogma was preceded by an RNA world in which RNA molecules carried both the genetic information and executed the gene functions (through ribozyme activity) is now widely accepted [130]. However, it is also well recognized that RNA due to its vulnerability to hydrolysis - especially as a result of catalysis by divalent metal ions - would not have been able to evolve in a harsh pre-biotic environment Also the formation of RNA under presumed pre-biotic conditions is extremely inefficient It is not so far-fetched to propose that a peptide nucleic acid-like molecule may have been able to function as a form of pre-biotic genetic material since it... 

The use of alkali and alkaline earth group metal ions, especially those of sodium, potassium, magnesium, and calcium, for maintenance of electrolyte balance and for signaling and promotion of enzyme activity and protein function are not discussed in this text. Many of these ions, used for signaling purposes in the exciting area of neuroscience, are of great interest. In ribozymes, RNAs with catalytic activity, solvated magnesium ions stabilize complex secondary and tertiary molecular structure. Telomeres, sequences of DNA at the ends of chromosomes that are implicated in cell death or immortalization, require potassium ions for structural stabilization. 

There are three mechanistic possibilities for catalysis by two-metal ion sites (Fig. 10). The first of these is the classic two-metal ion catalysis in which one metal plays the dominant role in activating the substrate toward nucleophilic attack, while the other metal ion furnishes the bound hydroxide as the nucleophile (Fig. 10 a). Upon substrate binding, the previously bridged hydroxide shifts to coordinate predominately with one metal ion. Enzymes believed to function through such a mechanism include a purple acid phosphatase [79], DNA polymerase I [80], inositol monophosphatase [81],fructose-1,6-bisphosphatase [82], Bam HI [83], and ribozymes [63]. 

Ribozymes are a class of metallo-enzymes based on RNA rather than proteins. They have potential in clinical medicine, for example, as potential anti-HIV agents (568, 569) and as possible new tools for the treatment of cancer (570). The active structures of ribozymes contain domains of stacked helices which pack together through tertiary contacts. Divalent metal ions such as Mg(II), Zn(II), and Mn(II) can tune the reactivity and shape the structures of ribozymes (571). Manganese(II) and Mg(II) have similar hexacoordinate ionic radii (0.86 and 0.97 A, respectively) (572) and octahedral geometry ( )Ka of hydrates Ca(II), 12.7 Mg(II), 11.4 Mn(II), 10.7 Zn2+, 9.6) (571). There are several potential oxygen donors on the ribose sugar moiety. 

Magnesium has its role intimately intertwined with phosphate in many phosphoryl transfer reactions, as Mg-ATP in muscle contraction, in the stabilization of nucleic acid structures as well as in the catalytic activity of ribozymes (catalytic RNA molecules). It also serves as a structural component of enzymes, and is found as the metal centre in chlorophylls, which absorbs light energy in photosynthesis. 

The intron group I ribozymes feature common secondary structure and reaction pathways. Active sites capable of catalyzing consecutive phosphodi-ester reactions produce properly spliced and circular RNAs. Ribozymes fold into a globular conformation and have solvent-inaccessible cores as quantified by Fe(II)-EDTA-induced free-radical cleavage experiments. The Tetrahy-mem group I intron ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand—the exon. This ribozyme also has been proposed to use metal ions to assist in proper folding, to activate the nucleophile, and to stabilize the transition state. ... 

Another naturally occurring ribozyme which catalyzes phosphodiester transfer reactions is the hairpin ribozyme. The hairpin ribozyme has been the subject of a number of excellent review articles [24,25]. Several independent studies performed recently have indicated that the hairpin ribozyme has an interesting feature which distinguishes it from the aforementioned ribozymes mechanistically While the HHR, the group I intron, the HDV ribozyme and many other ribozymes that we are going to meet in this review are metalloenzymes and require divalent metal ions in their active sites for functional group activation, divalent metals ions only play a passive role (they are mainly required for cor-... 

While indirect selections work quite well for antibodies they have been less successful in the case of catalytic nucleic acids. There are only three examples which prove that it is possible in principle to obtain a ribo- or deoxyribozyme by selecting an aptamer that binds to a TSA A rotamase ribozyme [7], a ribozyme capable of catalyzing the metallation of a porphyrin derivative [92], and one catalytic DNA of the same function [93]. Another study reported the selection of a population of RNA-aptamers which bind to a TSA for a Diels-Alder reaction but the subsequent screen for catalytic activity was negative for all individual RNAs tested [94]. The attempt to isolate a transesterase ribozyme using the indirect approach also failed [95]. 

In our recent study of reaction kinetics, we observed an unusual phenomenon when we analyzed the activity of a hammerhead ribozyme as a function of the concentration of Na ions on a background of a low concentration of either Mn or Mg ions [82]. At lower concentrations of Na ions, Na ions had an inhibitory effect on ribozyme activity, whereas at higher concentrations, Na ions had a rescue effect. We propose that these observations can be explained if we accept the existence of two kinds of metal-binding site that have different affinities. Our data also support the two-phase folding theory [77-80, Fig. 7], in which divalent metal ions in the ri-bozyme-substrate complex have lower and higher affinities, as proposed by Lilley and coworkers on the basis of their observations of ribozyme complexes in the ground state. 

Our data indicate that ribozyme activity in a low concentration of divalent metal ions decreases dramatically at lower concentrations of NaCl (Fig. 8). 

As the concentration of NaCl is increased after ribozyme activity has reached a minimum, the activity of the ribozyme is restored (Fig. 8). This rescue cannot be explained in terms of the number of bound Mn ions since the number does not increase at higher concentrations of NaCl, according to Horton et al., as described above. It is likely that, at higher concentrations, Na ions can work to fold the complex into the active structure and, as a result, more efficient Mn ions, even at limited concentrations, can work as a catalyst (see below for details). More efficient Mn ions can work as a catalyst even at a limited concentrations. As we would anticipate from the structural role and inefficient catalytic activity of Na ions, several groups have reported that ribozyme-mediated cleavage reactions can occur even in the absence of divalent metal ions provided that the concentration of monovalent ions, such as Na" ions, is extremely high [64-66]. 

A novel finding related to the mechanism of catalysis by the genomic HDV ribozyme is that the pKa of C75 is perturbed to neutrality in the ri-bozyme-substrate complex and, more importantly, that C75 acts as a general acid catalyst in combination with a metal hydroxide which acts as a general base catalyst (Fig. 9A) [105]. The discovery of this phenomenon provided the first direct proof that a nucleobase can act as an acid/base catalyst in RNA. As a result, as shown by the solid curve in Fig. 9B, the curve that represents the dependence on the pH of the self-cleavage of the precursor genomic HDV ribozyme has a slope of unity at pH values that are below 7 (the activity increases linearly as the pH increases, with a slope of +1). Then, at higher pH values, the observed rate constant is not affected by the pH. 

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