Circular structure

Biochemical and genetic experiments in yeast have revealed that the b poly(A) tail and its binding protein, Pablp, are required for efficient initiation of protein synthesis. Further studies showed that the poly(A) tail stimulates recruitment of the 40S ribosomal subunit to the mRNA through a complex set of interactions. Pablp, bound to the poly(A) tail, interacts with eIF-4G, which in turn binds to eIF-4E that is bound to the cap structure. It is possible that a circular structure is formed and that this helps direct the 40S ribosomal subunit to the b end of the mRNA. This helps explain how the cap and poly(A) tail structures have a synergistic effect on protein synthesis. It appears that a similar mechanism is at work in mammalian cells. 

DNA ligase is not only important in DNA replication it is also used to seal deoxyri-bonucleotide segments in the crossover events during gene recombination. The enzyme also functions to close breaks in segments of DNA undergoing repair and is required to join theends of mitochondrial DNA to form their characteristic circular structure. 

One class of laser resonators is based on circular structures like spheres, disks, and rings. In these structures, the optical modes form closed circular loops and... 

Mitochondrial DNA and the DNA of most prokaryotes are closed circular structures. These molecules may exist as relaxed circles or as supercoiled structures in which the heUx is twisted around itself in three-dimensional space. Supercoiling results from strain on the molecule caused by under- or overwinding the double helix ... 

Electron microscopy shows that DNA consists of either linear or circular structures. The chromosomal DNA in bacteria is a closed circle, a result of covalent joining of the two ends of the double helix (Figure 10.11). Note the presence of supercoils, branch points, intersections, and the generally thin and open structure. The chromosomal DNA in eukaryotic cells, like ours, is believed to be linear. 

I I Electron micrographs of the E. coli chromosome sug-jj gcst a folded circular structure containing about 40-f 100 supercoiled loops (diagrammatically indicated in fig. 25.16). It is believed that the folded structure is held together by an RNA-protein core, although the manner in which this is done is not well understood. The structure is further stabilized because the core forms a complex with positively charged polyamines and certain basic proteins. D. E. Pettijohn and his co-workers have provided evidence of such a core. They first showed that the individual super-... 

Simulated autoradiographs of the E. coli chromosome after one or more replications in the presence of [3H]thymidine. After one round of replication, the autoradiograph shows a circular structure that is uniformly labeled. The second round of replication begins with the formation of a replication eye. One branch in the replication eye is twice as strongly labeled as the remainder of the chromosome, indicating that this branch contains two labeled strands. This structure is consistent with semiconservative replication for the E. coli chromosome. 

Catenane. An interlocked pair of circular structures, such as covalently closed DNA molecules. 

In proteins with a symmetric structure, circular permutation can account for the shift of active-site residues over the course of evolution. A very good model of symmetric proteins are the (/Ja)8-barrel enzymes with their typical eightfold symmetry. Circular permutation is characterized by fusion of the N and C termini in a protein ancestor followed by cleavage of the backbone at an equivalent locus around the circular structure. Both fructose-bisphosphate aldolase class I and transaldolase belong to the aldolase superfamily of (a/J)8-symmetric barrel proteins both feature a catalytic lysine residue required to form the Schiff base intermediate with the substrate in the first step of the reaction (Chapter 9, Section 9.6.2). In most family members, the catalytic lysine residue is located on strand 6 of the barrel, but in transaldolase it is not only located on strand 4 but optimal sequence and structure alignment with aldolase class I necessitates rotation of the structure and thus circular permutation of the jS-barrel strands (Jia, 1996). 

Beginning with diethynylbenzene derivatives, it is obvious that the para-isomer 45 could lead to rod-like hydrocarbons, whereas the meta- (46) and the ortho-isomers (47), respectively, could provide angular and circular structures. Of course, an increase in the number of ethynyl groups results in an increased number of coupling possibilities. 1,3,5-Triethynylbenzene (48), for example, is of interest since it can be used for the construction of bicyclic hydrocarbons - it constitutes a blown-up version of a bridgehead. Clearly, hexa-ethynylbenzene (49) [32] can function as a tile for the preparation of novel forms of... 

The term chromosome refers to a physical or organizational unit within which part of or all the genome is contained. Thus, the E. coli genome is contained within just one chromosome, comprising a single DNA molecule. It has a size of 2.5 x 109 Da and contains approximately 4.6 x 106 base pairs. The size of DNA molecules is more commonly expressed in kilobase pairs (kb, 1,000 base pairs). The E. coli chromosome is 4,639 kb in size. Another feature of this particular molecule is that it is a closed, or circular, structure, i.e., there are no free ends. 

A chromosome contains a single DNA molecule, which is generally very large e.g., some bacterial chromosomes are composed of as many as 4 x 106 base pairs. Furthermore, in many cases, the DNA is a closed or circular structure. Some bacterial chromosomes are linear. We will concentrate first on the topology of replication of the circular bacterial ( . coli) chromosome. Little is known about linear bacterial chromosomes in this regard. 

Figure 5. a-Carbon structure of Eco RI endonuclease-DNA complex. The left part shows a front view with double-stranded DNA (heavier white lines running vertically through center) setting in the crevice formed by the two subunits of the enzyme. The right part is a projection from the "top" with axis 90° from that on the left. (The double-stranded DNA is the circular structure at bottom center.) (Reproduced with... 

Dugaiczyk, A., Boyer, H. W., and Goodman, H. M. (1975). Ligation of EcoRI Endonuclease-Generated Fragments into Linear and Circular Structures. J Mol Biol 96 171. 

Figure 6. Electron micrograph of Beulah lignite showing organic region enriched in sodium (circular structure in lower center of view).

Similar results were obtained for data sets CYCOO and CYCOl. The presence of outliers degrades the results of the classical PCA considerably, and the intentionally designed circular structure in the plane no longer exists. In contrast, PP PC s do not change very much and the circular pattern is retained both with and without the outliers. 

FIGURE 3.3 Circular structure of a sustainable economy (Stahel, 2008). 

Two related circular structures have been described recently by Lehn [68] and McCleverty and Ward [69]. The segmental ligand 36 reacts with copper(I) to form a circular dodecanuclear species [Cu]2(36)4] shown in Figure 18 [68]. The metal... 

Bacteriophage X is a genetically complex and extensively studied virus of E. coli. Because it has been the object of molecular genetic research, it was investigated and developed as a vector. The DNA of phage X, in the form in which it is isolated from the phage particle, is a linear duplex molecule of about 45.5 kb pairs. The entire DNA sequence has been determined (SI). At each end are short, single-stranded 5 projections of 12 nucleotides that are complementary in sequence and by which the DNA adopts a circular structure when it is injected into the host cell i.e., X DNA naturally has cohesive termini that associate to form the cos site. 

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