RNA model

When working as a guest at the famous Salk Institute for Biomedical Research in La Jolla (California), Eschenmoser (now a professor emeritus) was able to study a series of sugar derivatives as possible candidates for pre-RNA models. It turned out that five atoms in the nucleic acid chain suffice, if they are present in an optimal extended form. This was shown using a polymer containing (L)-a-threofuranosyl-(3 2 )-oligonucleotides (TNA) (Fig. 6.18) (Schoning et al., 2000). 

Fig. 2. Secondary structure of the E. coli 16 S RNA. Model Berlin according to Glotz and Brimacombe (1980) California according to Woese et al. (1980) Strasbourg according to Stiegler et al. (1981). For details see Brimacombe et al. (1983). Here and in Figs. 3 and 13, section a of each structure includes the 5 end of the molecule, which is marked b includes the middle portion and c includes the marked 3 end. Arrows indicate connections between a, b, and c. Reproduced with permission from Brimacombe et al. (1983).

Bnilding on the fonndation of these stndies, Haddad et al. used rings I and II of paromomycin (called paromomine) as the minimum structural motif in a computational search of over 273,000 componnds that might bind an A-site template. Results of this search were then narrowed based on steric and energetic demands. Several componnds were snbseqnently synthesized and shown to bind to an RNA model of the A-site, with some of the compounds (e.g., 2) exhibiting broad-spectrum activity in bacteria. X-ray strnctnres with the RNA models and with the 30S ribosome vindicated the design principles. The compounds do bind to the A-site and they do flip the two bases mentioned previously to the extrahelical position, as do other antibiotics of this class. 

Hampel, A., Tritz, R., Hicks, M. and Cruz, P. (1990) Hairpin catalytic RNA model evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res., 18, 299-304. 

Many artificial systems have been designed recently to imitate the function and behaviour of native enzymes - biomimetic chemistry [27]. Among them, calixarene-based receptors bearing one, two or three Zn(II) complexes on the upper rim were prepared as a model for phosphoesterases [28-31]. Dinuclear receptor 25 was reported to enhance the rate of transesterification of the RNA model substrate 2-hydroxypropyl-p-nitrophenyl phosphate more than 20,000 times compared with the non-catalysed reaction. The complexation mode for the phosphate anion can be described as cascade complexation where the anion is coordinated within the cavity formed by two zinc cations. 

Structure RNA Models to Three-Dimensional Shape Models 243... 

Low-Resolution Atomic Scale Models of RNA [X Fitting Secondary Structure RNA Models to Three-Dimensional Shape Models... 

For transition metals and Zn(II), how might metal complexes be designed to promote rapid cleavage of RNA One approach is the functionalization of ligands to participate in catalysis. The N-methyl-CR ligand was modified to contain a basic group for bifunctional catalysis (21). A Zn(II) complex of one of the modified macrocycles was shown to accelerate cyclization of the RNA model substrate 1 (1 = 4-nitrophenylphosphate ester of propylene glycol) 20-fold more rapidly than the Zn(II) complex of N-methyl-CR. 

Modified nucleosides incorporated into small RNA model systems can also be used to investigate the global versus individual effects of modified nucleotides on natural RNAs, such as rRNA or tRNA. For example, in some early studies, Yarian et al. (44) demonstrated that pseudouridine (Table 1) leads to increased thermal stability of the tRNA anticodon stem-loop region. Later, Meroueh et al. (45) demonstrated that pseudouridines have opposing effects on rRNA helix 69 stability, which depends on their specific locations and sequence contexts. These effects on stability may be important for conformational switching mechanisms in functional RNAs (46, 47). 

In recent years, methods for the catalytic cleavage of the P-O bond in phosphate esters have been developed. It is now reported that a cyclic P-sheet peptide -based binuclear zinc (II) complex markedly accelerated the cleavage of the phosphodiester linkage of the RNA model substrate 2-hydroxypropyl p-nitro-phenyl phosphate (102) (Scheme 17). °... 

Other authors found that a highly flexible crown ether - scaffold (103) constitutes a simplified activity - controllable catalytic system for phosphodiester bond cleavage of the same RNA model substrate (102). ... 

A zinc complex of the BPAN (2,7-bis[2-(2-pyridylethyl)aminomethyl]-l,8-naphthyridine ligand, [(BPAN)Zn2(p-0H)(p-Ph2P02)](C104)2, Fig. 27) catalyzes the transesterification of the RNA model substrate HPNP (2-hydroxypropyl 4-nitro-phenyl phosphate (Fig. 40, bottom) in aqueous buffered solution (HEPES) containing 1% CH3CN.141 The rate of this reaction was found to be 7 times fast than the reaction catalyzed by a mononuclear Zn(II) complex of bpta (Fig. 25). A pH-rate... 

Fig. 15. Cooperativity of two Cu ions in the covalent binuclear complex 13 for cleaving RNA models.

The overall efficiency of these nonmolecular bimetallic sysems to promote phosphate ester hydrolysis was illustrated with ApA as RNA model (0.1 mM) hydrolysis occurred with a mixture of LaCls and FeCls (10 mM each) to more than 70% at 50°C and neutral pH in 5 min (351). The products of the reaction included adenosine and 2 -and 3 -monophosphate adenonsine, indicating that the mechanism involved a first trans-esterification step by the vicinal 2 -OH of ribose. With the same mixture of metal ions, the DNA model TpT (0.1 mM) (Fig. 18), left, B = thymine) was converted to thymidine and 3 - and 5 -monophosphate th5miidine with 36% of conversion in 24 hr at 70°C at neutral pH. The important point is the notion of cooperativity between the two metals. 

RNA model substrate 19. The kinetics indicated bifunctional catalytic effects for 68-CU2 and that at the pH optimum of 7.4 at least one amine is protonated, which could assist as a general acid in the binding and activation of the substrate (99JOC6337). 

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