Base-specific cleavage reactions chemistry

Based on chemical considerations alone, ribozymes should be able to catalyze many different types of reactions. Ribozymes can maintain defined secondary and tertiary structures, just as protein enzymes do. Ribozymes can interact with substrates specifically via hydrogen bond networks, just as protein enzymes do. Finally, ribozymes have available to them a chemistry that, while more limited than of proteins, is substantial. RNA contains proton donors and acceptors with pK, values that cluster at 4 and 9.71 The critical lack of a good donor/acceptor with a pKt near 7 can be rectified by any of several simple expedients, such as modification of guanosine to 7-methylguanosine, protonation of triple base-paired cysto-sine,72 or inclusion of a proton donor/acceptor in an environment with a different polarity than water (in this respect, it is interesting to note that Dahm and Uhlenbeck have found that the cleavage reaction catalyzed by the hammerhead ribozyme is dependent on some dissociable proton with a pKa of 8.0).73... 

Af -2,2-Bis(ethoxycarbonyl)vinyl-protected amino acids are prepared by reaction of commercially available diethyl 2-(ethoxymethylene)malonate (127) with the respective amino acid in methanolic KOH. This rapid reaction is complete within 5 minutes and leads to the potassium salts. Subsequent acidification with 1M HCl yields the amino acid derivative in 75-90% yield.f This intermediate enamine-type N-protection is of particular interest in chemistry to be performed on the carboxy groups of the amino acids such as esterification with alkyl bromides in the presence of a base. Since cleavage of the enamine entity is achieved by treatment with bromine in chloroform at room temperature, it cannot be used for amino acids sensitive to halogenation such as tyrosine, tryptophan, and methionine (Scheme 61). Based on the experience gained with the enamine-type protection the Al-2-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl (Dde) and N-2-(4,4-dimethyl-2,6-dioxocyclohex-ylidene)isovaleryl derivatives were developed as specific side-chain protecting groups (see Section 2.1.2.2.5.2). 

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