摘要:

Since its theoretical inception, the tRNA molecule has been identified and many of its functions have been described in terms of its structure. However, the molecular basis for the aminoacylation specificity of tRNA has remained largely unsolved until recently, when substantial progress has disclosed fundamental aspects of this process. What we know and would like to know about tRNA identity will be outlined, as will the experimental approaches used in this research.— McClain, W. H. Transfer RNA identity.FASEB J.7: 72‐78; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422977

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

Our present understanding of the molecular mechanisms responsible for the recognition of tRNAs by their cognate aminoacyl‐tRNA synthetases (aaRS) is essentially based on three sources of information:1) the characterization of tRNA identity determinants using in vivo and in vitro approaches,2) the classification of synthetases from primary sequence analysis: aaRS can be partitioned into two classes according to the spatial structure of their ATP binding domain, and3) the structural results of crystallographic investigations and solution studies. The crystal structures of three aaRS and two complexes, one of each class, are known to atomic resolution. tRNA recognition has two structural components. The interaction between the acceptor end and the active site domain is class‐specific and the binding mode of the stem observed in the crystal structures of GlnRS‐tRNAGlnand AspRS‐tRNAspcomplexes can be generalized to their respective classes. Identity determinants located in other parts of the tRNA molecule are decoded by different domains of the enzyme. These protein modules exhibit a large structural diversity. The recognition process is then system or subgroup specific.— Gavarelli, J., Moras, D. Recognition of tRNAs by aminoacyl‐tRNA synthetases.FASEB J.7: 79‐86; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422978

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

The extent to which ribosomal RNA is directly involved in the function of ribosomes has important implications for both the mechanism of translation and the molecular origins of life. Detailed evidence has accumulated that places the anticodon and acceptor ends of tRNA in close proximity to conserved features of rRNA in the ribosome. Recent studies are providing evidence that these features are important for ribosomal function.— Noller, H. F. tRNA‐rRNA interactions and peptidyl transferase.FASEB J.7: 87‐89; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422979

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

The modification of phosphate into phosphorothioate internucleotidic linkages in various RNAs and their usefulness in identifying phosphate positions essential for function are described. Several modifications of the 2′‐hydroxyl group of the ribose, particularly the replacement by fluorine atoms and amino groups, is discussed. These studies have been concentrated on hammerhead ribozymes in order to determine hydroxyl groups important for the catalytic activity. In addition these derivatives have been instrumental in rendering ribozymes more stable toward nucleases.—Heidenreich, O., Pieken, W., and Eckstein, F. Chemically modified RNA: approaches and applications.FASEB j 7: 90‐96; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.7678566

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

The limited number of RNA structures determined by X‐ray crystallography and NMR spectroscopy compels the use of experimental and theoretical methods that are less precise to obtain information on RNA conformation. RNA flexibility, a consequence of rotational freedom about seven intra‐ and internucleotide bonds, is unfortunately of such magnitude that these alternate techniques fall short of providing sufficient information to build robust tertiary structures. Various RNA modeling methods, described herein, permit the organization of this structural data to the form of three‐dimensional structures. Interactive computer graphics techniques, for example, have generated several useful models. Also, conventional computer algorithms involving the minimization of empirical energy functions, previously limited to small molecules, are giving way to methods able to handle much larger molecules. Modified distance geometry and molecular mechanics algorithms, using simplified “pseudoatom” representations, can generate structures consistent with input data. A constraint satisfaction algorithm combined with discrete representations of nucleotide conformations systematically explores poorly defined regions of a molecule yielding all‐atom representations, but requires enough structural constraints to avoid a computational explosion.— Gautheret, D., and Cedergren, R. Modeling the three‐dimensional structure of RNA.FASEB J.7: 97‐105; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.7678567

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

In vitro selection and in vitro evolution methods represent powerful tools for isolating functional RNA molecules, and are proving to have wide applications in biology. Selection in the absence of living cells is possible because some RNA molecules possess a selectable “phenotype” (catalytic activity or ligand binding) as well as a “genotype” (nucleotide sequence). This review discusses the basic principles of in vitro selection technology and the application of these methods to isolate RNA molecules with interesting and novel properties. Selection techniques have been used to analyze the structure and function of catalytic RNA molecules (ribozymes), and to isolate novel catalytic structures not found in nature. They are also useful for studying protein‐RNA interactions and for isolating RNA molecules that bind specifically to peptides and other ligands. The isolation of RNA molecules with new binding functionalities (aptamers) for both large and small molecules has exciting potential for discovery of new drugs and diagnostic reagents.— Burke, J. M., and Berzal‐Herranz, A. In vitro selection and evolution of RNA: applications for catalytic RNA, molecular recognition, and drug discovery.FASEB J.7: 106‐112; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422956

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.— Olsen, G. J., Woese, C. R. Ribosomal RNA: a key to phylogeny.FASEB J.7: 113‐123; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422957

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

In elucidating the part played by the essential stem structures (I, II, and III) in the self‐cleavage activity of genomic HDV ribozyme, several point and compensation variants were constructed on pseudoknot‐like structure by site‐directed mutagenesis. The self‐cleavage activities of these variants indicated that stems I and III were essential for the activity by forming Watson‐Crick base pairs. On the other hand, disruption of A704:U767 had little influence on the cleavage activity, indicating that it is not essential in forming an active structure. Also, our V1 nuclease probing studies showed that the A704U and HDV88 variants have a sensitivity similar to the nuclease, and major cuts are visible in the stem I and stem II regions. Thus, stem I and stem II regions are maintained together with stem III regions in both molecules. These results and our earlier site‐directed mutagenesis studies strongly support a pseudoknot‐like structure for the genomic HDV ribozyme.— Kumar, P. K. R., Suh, Y.‐A., Taira, K., Nishikawa, S. Point and compensation mutations to evaluate essential stem structures of the genomic HDV ribozyme.FASEB J.7: 124‐129; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422958

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

A chemical modification‐interference assay was used to evaluate the sequence requirements for self‐cleavage of a 73‐nucleotide self‐cleaving RNA from the genomic hepatitis delta virus (HDV). Twenty‐two nucleotides were categorized as individually essential for self‐cleavage, shown by loss of activity when modified. All of these required nucleotides fell within 38 nucleotides downstream of the cleavage site, suggesting an essential structural or functional role for this region. Lesser effects were seen for nucleotides further 3′ of the cleavage site, and a small number of nucleotides had a negligible effect on the extent of self‐cleavage when modified. Several modifications increased the extent of self‐cleavage, suggesting these nucleotides may act to inhibit the reaction when unmodified. The functional requirements for certain nucleotides are discussed in the light of structural probing data and conventional mutational analysis available for other HDV RNAs.— Belinsky, M. G., Britton, E., Dinter‐Gottlieb, G. Modification interference analysis of a self‐cleaving RNA from hepatitis delta virus.FASEB J.7: 130‐136; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422959

出版商:Wiley    

年代:1993

数据来源: WILEY

摘要:

To elucidate the role of the Mg2+ion in ribozyme reactions, we carried outab initiomolecular orbital investigations on dianionic trimethoxyphosphoraneAand its Mg2+complex (overall a neutral molecule) as a model system for the reaction center ofTetrahymena‐type ribozyme. Although dianionic oxyphosphoraneAconcentrates its negative charges on the equatorial phosphoryl oxygens, the coordination of the Mg2+ion between these two oxygens is unlikely. Geometry optimizations of the complex and the electrostatic potential ofAboth suggest that Mg2+coordination preferably occurs in the region between the axial oxygen and the equatorial phosphoryl oxygen. The considerations of electrostatic potential rationalize the geometries of carboxylate‐metal and phosphate‐metal interactions extracted from the Cambridge Structural Database as well. Consequently, the Mg2+ion at the active site ofTetrahymena‐type ribozyme most likely lies in the regions between the axial and equatorial oxygens. The axial‐equatorial coordinations of Mg2+ions conceivably increase the electronegativities of the axial oxygens and facilitate cleavage of the phosphodiester bond located at the junction of the intron and the exon. It is thus likely that the Mg2∗ ions play the key role in the phosphodiester cleavage reactions mediated by ribozymes.— Uchimaru, T., Uebayasi, M., Tanabe, K., Taira, K. Theoretical analyses of the role of Mg2+ions in ribozyme reactions.FASEB J.7: 137‐142; 1993.

ISSN:0892-6638    

DOI:10.1096/fasebj.7.1.8422960

出版商:Wiley    

年代:1993

数据来源: WILEY