Ribozyme catalytic properties

Sidney Altman discovered this property of RNA in the course of studies on precursor transfer RNA. It was realized that the catalytic properties of RNA are not exactly the same as those of protein enzymes, since the ribozyme is itself active and thus undergoes change during the catalytic reaction. This does not correspond to the generally accepted definition of an enzyme. Later studies, however, showed that some ribozymes are capable of acting catalytically at other RNA molecules. The ribozymes remain completely unchanged in this process, and thus fulfil the definition of a real enzyme. 

Since the discovery that RNA molecules can possess catalytic activities, ribozymes have become a fascinating field both for academic researchers and the pharmaceutical industry. In this review, we emphasize the latest progress made in structure determination of ribozymes as well as the generation of DNA and RNA enzymes with novel catalytic properties by combinatorial approaches. 

The discovery in the 1980s that RNA molecules often have catalytic properties and may serve as true enzymes (ribozymes Chapter 12) stimulated new thinking about evolution. Although RNA catalysts are not as fast as the best enzymes they are able to catalyze a wide variety of different reactions. Could it be that in the early evolution of organisms RNA provided both the genetic material and catalysts The "RNA world" would have been independent of both DNA and protein.a b Later DNA could have been developed as a more stable coding molecule and proteins could have evolved as more efficient catalysts. Plausible reactions by which both cytosine and uracil could have arisen in drying ponds on early Earth have been demonstrated.6... 

Self-splicing KNA. The precursor to the 26S rRNA of Tetrahymena contains a 413-nucleotide intron, which was shown by Cedi and coworkers to be selfsplicing, i.e., not to require a protein catalyst for maturation.581 582 This pre-rRNA is a ribozyme with true catalytic properties (Chapter 12). It folds into a complex three-dimensional structure which provides a binding site for free guanosine whose 3-OH attacks the phosphorus at the 5 end of the intron as shown in Fig. 28-18A, step a. The reaction is a simple displacement on phosphorus, a transesterification similar to that in the first step of pancreatic ribonuclease action (Eq. 12-25). The resulting free 3-OH then attacks the phosphorus atom at the other end of the intron (step b) to accomplish the splicing and to release the intron as a linear polynucleotide. The excised intron undergoes... 

The secondary double-reciprocal plot of the data from Figure 5.3.5 gives Mi-chaelis constants of 0.37 mM for the diene and 8 nm for the dienophile. The calculated maximum rate Vmax is 0.15 mM min-1, which at a ribozyme concentration of 7 xm corresponds to a kcat of 21 min-1. The highest initial rate that was measured directly corresponds to a catalytic turnover of approximately 6 min-1. With these catalytic properties the 49nt Diels-Alderase ribozyme is among the faster... 

Perhaps even more esoteric than antisense nucleic acids are RNA molecules that are able to specifically cleave other RNA molecules. Until several years ago, it was generally thought that all cellular processes were dictated by DNA through the structure of polypeptides, which performed all the functions. During studies conducted on RNA, it was discovered that some RNA strands had catalytic properties. These nonprotein biocatalysts are referred to as ribozymes and combine the properties of antisense RNA with the ability to cleave target RNA. 

Libraries produced by microorganisms or through biochemical techniques have been frequently used to find either peptidic or oligonucleotidic sequences that bind certain receptors, or enzymes, and/or possess catalytic properties (catalytic antibodies and ribozymes, among others). Biological libraries can also be produced by combinatorial... 

Figure 10.40 Selection of artificial ribozymes with catalytic properties for a Diels-Alder reaction from the biosynthetic ON modified ribozyme library L28 library synthesis and the selection process using the biotinylated selection dienophile 10.60.

Tsang, J., and Joyce, G.F. Evolutionary optimization of the catalytic properties of a DNA-cleaving ribozyme. Biochemistry 33 5966-5973, 1994. 

Based on their observations, they concluded that the ribosome is ribozyme and directs the catalytic properties of its all-RNA active site. The secondary structures of both 5S and 23S rRNA from H. marismortui are remarkably close to those deduced for them by phylogenetic comparison. 

Proteins are not the only biological molecules with catalytic properties. Some RNAs, called ribozymes, also catalyze certain reactions. 

The transition state of Diels-Alder reaction of diene 56 with dienophile 57 to give the adduct 58 (Scheme 5.14) is a boat-like type. The antibody 39-Al 1, generated to the bicy-clo [2.2.2 ] octane hapten 59 that mimics the transition state of the reaction, efficaciously catalyzed the cycloaddition, selectively giving 58 in buffered aqueous medium (Scheme 5.14). ° Ribozymes are RNA molecules with catalytic properties. Artificial ribozymes, isolated fi om synthetic combinatorial libraries, accelerate a broad range of reactions including the Diels-Alder cycloaddition. These ribozymes generally require that at least one of the reactants be RNA or be covalently tethered to RNA. 

Strand (57). Other problems such as the formation of G-quadruplexes by G-rich template strands, and non-Watson-Crick base pairings (e.g., G-U wobble pairing) further inhibit high-fidelity sequence transfer in template-directed synthesis. These problems would greatly restrict the sequence space for evolving ribozymes and proto-ribozymes as newly mutated sequences that possess new catalytic properties may not be replicable (i.e., heritable). 

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