RNA circles

RNA carries out its enzymic roles with many fewer chemical resources than its protein counterparts it has a ribose-phosphate backbone (Chap. 3), with four rather similar heterocyclic nucleobases, plus attendant water molecules and metal ions. They carry out the water-elimination condensation reactions in splicing certain classes of introns (Chap. 7) and in the site-specific cleavage and ligation of small replicating RNA circles in some species of organism. 

Figure Bl.9.9. Comparison of the distance distribution fiinction p(r) of a RNA-polymerase core enzyme from the experimental data (open circle) and the simulation data (using two different models). This figure is duplicated from [27], with pennission from Elsevier Science.

In 4>X174, however, replication begins with a single stranded closed circle, a rather atypical situation. First, primase brings about the synthesis of a short RNA primer, beginning at one or more specific initiation sites on the DNA. 

Figure 3.3 Chemical structure of (a) ribose and (b) 2 -deoxyribose, the nucleotide pentoses found in RNA and DNA respectively. The differences in chemical structure are highlighted by the dotted circles...

A Anaerobic adaptation was obtained by flushing the cells with argon. At indicated time points, samples were taken to measure the in vitro Fk-ase activity of C. reinhardtii (box), S. obliquus (circle), C. fusca (triangle), C. moewusii (diamond). While the activities of both Scenedesmus species are comparative low, the in vitro H -production rate of anaerobically induced C. moewusii cultures is 2 times higher than the activity of induced C. reinhardtii cultures. B Northern blots with equal amounts of total RNA isolated from an anaerobically adapted culture (2 h) and an uninduced reference culture (0 h) of C. moewusii. The upper blot was incubated with a RNA sample of the 3 UTR of the hydA 1 cDNA, while the lower blot was incubated with a RNA sample generated of the cDNA from the constitutively expressed sedoheptulose 1,7-bisphosphatasegene. 

Fig. 1. Nucleotide sequence of the SFV 26 S RNA (top row), the corresponding amino acid sequence (middle row), and the amino acid sequence of the Sindbis virus structural proteins (bottom row). Nucleotides are numbered from the 5 end of the RNA molecule and all amino adds from the amino terminus of each protein. The amino- and the carboxyl-terminal ends of each protein are indicated hy arrows, glycosylation sites by triangles, and membrane-spanning regions of the viral glycoproteins by underlines for Sindbis virus and overlines for SFV. Amino acids in boxes are negatively charged (Asp and Glu), and those circled are positively charged (Lys and Arg). Some restriction endonuclease cleavage sites are shown on the nucleotide sequence. The alignment of the amino acid...

Fig. 10A pL (L=H or D) profiles of hairpin ribozyme of the native sequence of and 2,6-diaminopurine at position 8 [119]. The native sequence in H2O and in D2O are represented hy filled diamonds and filled squares, respectively. 2,6-diaminopurine at position 8 in H2O and in D2O are represented by open circles and open triangles, respectively. B Proposed catalytic mechanism. RNA cleavage catalyzed by the keto-enol tautomeriza-tion of Gg is achieved by a abstraction of a proton from the N1 to the 5 -0 leaving group [119]... 

In this chapter we examine the synthesis of RNA on a DNA template and the postsynthetic processing and turnover of RNA molecules. In doing so we encounter many of the specialized functions of RNA, including catalytic functions. Interestingly, the substrates for RNA enzymes are often other RNA molecules. We also describe systems in which RNA is the template and DNA the product, rather than vice versa. The information pathways thus come full circle, revealing that template-dependent nucleic acid synthesis has standard rules... 

These synthetic knots are such good substrates for type I topoisomerases that we constructed an RNA trefoil knot to seek RNA topoisomerase activity, which was suspected, but unknown. We designed the knot similarly to the DNA trefoil knot, and made the circle of the same sequence by altering the length of the linker used in the ligation. We discovered that topo HI is capable of catalyzing RNA strand-... 

Figure 5-30 Schematic cloverleaf structure of a phenylalanine-specific transfer RNA (tRNA he) of yeast. The dots represent pairs or triplets of hydrogen bonds. Nucleosides common to almost all tRNA molecules are circled. Other features common to most tRNA molecules are also marked. The manner in which the anticodon may be matched to a codon of mRNA is indicated at the bottom.

FIGURE 28.11 Phenylalanine tRNA from yeast, (a) A schematic drawing showing the sequence of bases. Transfer RNAs usually contain a number of modified bases ( gray circles). One of these is a modified guanosine (G ) in the anticodon. Hydrogen bonds, where present, are shown as dashed lines, (b) The structure of yeast tRNAphe as determined by X-ray crystallography. 

Identity elements in four tRNAs. Each circle represents one nucleotide. Filled circles indicate nucleotides that serve as recognition elements to the appropriate aminoacyl-tRNA synthase. It is possible that other identity elements occur in these structures that are still to be discovered. (From L. H. Schulman and J. Abelson, Recent excitement in understanding transfer RNA identity, Science 240 1591, June 17, 1988. Copyright 1988 by the AAAS. Reprinted by permission.)... 

Unlike the double-stranded nature of DNA, RNA molecules usually occur as single strands. This does not mean they are unable to base-pair as DNA can. Complementary regions within an RNA molecule often base-pair and form complex tertiary structures, even approaching the three-dimensional nature of proteins. Some RNA molecules, such as transfer RNA (tRNA) possess several helical areas and loops as the strand interacts with itself in complementary sections. Other hybrid molecules such as the enzyme RNase P contain protein and RNA portions. The RNA part is highly complex with many circles, loops, and helical regions creating a convoluted structure. 

Fig. 18.3. Raman spectral analysis of foetal osteoblast (FOB) differentiation. Unsupervised PCA of FOB cells cultured for 3 days in bioactive glass (BG) conditioned media (triangle) or control media (circle) (a). BG-treated cells formed a distinct cluster separate from control cells after 3 days culture. Least square (LS) analysis (which decomposes the cell spectra into the linear combination of Raman spectra obtained from the pure chemical constituents of the cell, e.g. nucleic acid, proteins, lipids, phospholipids and carbohydrates) of the relative RNA concentration of FOBs cultured for 1, 3 and 14 days in culture media (black) or BG condition media (grey), revealed a significantly reduced relative RNA concentration in FOBs culture in BG-conditioned media (b). FOBs cultured in BG-conditioned media appeared to accelerate FOB differentiation into mature adult osteoblast phenotypes (parallel gene and protein expression experiments confirmed this). Significant difference to control (p <0.05) [38]...

Fig. 3. RNA editing of the 5-HT2C receptor. RNA editing sites of the human 5-HT2C receptor are shown by black circles.

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