Nucleic acids of viruses

These studies demonstrated that (1) even a relatively minor chemical modification e.g., introduction of a 5-mercapto group into the cytosine base of 1 out of 100 nucleotide units) can convert a functional DNA or RNA template into a potent, competitive inhibitory analogue (antitemplate) which will bind to the template site of a polymerase either reversibly or irreversibly, and (2) even such antitemplates that are not made to be specific structural analogues of a natural template e.g., MPC) can differentiate between various polymerases. However, there are already some indications that antitemplates more closely related to the natural template of a given polymerase are more effective inhibitors of the latter, and it is expected that modified nucleic acids of viruses and tumors will show even much greater selectivities toward the corresponding reverse transcriptases in the presence of their endogenous templates. 

Structure viral-coat proteins Sheath around nucleic acid of viruses... 

Wilson, H.R. Diffraction of X-rays by Proteins, Nucleic Acids and Viruses. London Edward Arnold, 1966. 

Early steps in replication of the virus nucleic acid, in which the host cell biosynthetic machinery is altered as a prelude to virus nucleic acid synthesis. Virus-specific enzymes may be made ... 

At the far left, we can see the nucleic acid and protein structures shown in frame 1. In addition, we show a much larger protein, the immunoglobulin G antibody molecule. Four separate polypeptide chains join to make up an antibody molecule two heavy chains (blue) of about 400 amino acids and two light chains (purple) of about 200 amino acids. The antibody is about 16 nm in width. Finally, at the far right, we show the core particle from a small plant virus, the reovirus. Only the icosahedral protein coat of the virus can be seen. The reovirus particle is about 60 nm across. The nucleic acids of the virus are sequestered inside the virus core. The reovirus family is unusual in that its nucleic acids are all double-stranded RNA molecules. 

The term nucleoside was originally proposed by Levene and Jacobs in 1909 for the carbohydrate derivatives of purines (and, later, of pyrimidines) isolated from the alkaline hydrolyzates of yeast nucleic acid. The phosphate esters of nucleosides are the nucleotides, which, in polymerized forms, constitute the nucleic acids of all cells.2 The sugar moieties of nucleosides derived from the nucleic acids have been shown, thus far, to be either D-ribose or 2-deoxy-D-eri/fAro-pentose ( 2-deoxy-D-ribose ). The ribo-nucleosides are constituents of ribonucleic acids, which occur mainly in the cell cytoplasm whereas 2-deoxyribo -nucleosides are components of deoxypentonucleic acids, which are localized in the cell nucleus.3 The nucleic acids are not limited (in occurrence) to cellular components. They have also been found to be important constituents of plant and animal viruses. 

X-ray and neutron diffraction patterns can be detected when a wave is scattered by a periodic structure of atoms in an ordered array such as a crystal or a fiber. The diffraction patterns can be interpreted directly to give information about the size of the unit cell, information about the symmetry of the molecule, and, in the case of fibers, information about periodicity. The determination of the complete structure of a molecule requires the phase information as well as the intensity and frequency information. The phase can be determined using the method of multiple isomor-phous replacement where heavy metals or groups containing heavy element are incorporated into the diffracting crystals. The final coordinates of biomacromolecules are then deduced using knowledge about the primary structure and are refined by processes that include comparisons of calculated and observed diffraction patterns. Three-dimensional structures of proteins and their complexes (Blundell and Johnson, 1976), nucleic acids, and viruses have been determined by X-ray and neutron diffractions. 

The ability of the purification process to eliminate product related or host cell derived proteins, nucleic acid, carbohydrates, viruses, or other undesirable impurities, including undesirable media derived and chemical components, must be thoroughly investigated, as well as the reproducibility of the process. 

The technique is applicable to a wide range of samples which includes proteins, enzymes, nucleic acids and viruses, and is not limited by the size of the molecules. 

In protein crystals, due to the large size of the molecule, the empty space can have cross sections of 10-15 A or greater. The empty space between the protein molecules is occupied by mother liquor. This property of protein crystals, shared by nucleic acids and viruses, is otherwise unique among the crystal structures. In fact, the values of the packing coefficient of protein crystals range from 0.7 to 0.2, but the solvent molecules occupy the empty space so that the total packing coefficient is close to 1 [37]. Nevertheless, a detailed theoretical study has been carried out to examine the models of DNA-DNA molecular interactions on the basis of hard-sphere contact criteria. The hard-sphere computations are insufficient for qualitative interpretation of the packing of DNA helices in the solid state, but... 

Crystal-structure determinations provide atomic coordinates of proteins, nucleic acids, and viruses. Computational studies of these data — using both purely-numerical techniques and interactive graphics — seek the principles of structure, dynamics, function and evolution of living systems at the molecular level. 

X-ray crystallographers have now determined the structures of approximately one hundred biological macromolecules — proteins, nucleic acids, and viruses — to atomic resolution. These investigations have demonstrated that, unlike synthetic polymers, the biological molecules have specific three-dimensional conformations. Indeed, all information required to specify the structure of a protein is contained in the sequence of amino acids, and therefore the structure is also implicit in the sequence of nucleotides in the DNA or RNA genome. Analysis of the structures has provided explanations of their biological functions, and has revealed that there are recurrent architectural themes in their de-sign (J, 2). 

In the polishing phase the focus is almost entirely on high resolution to achieve final purity. Most contaminants and impurities have already been removed except for trace impurities such as leachables, endotoxins, nucleic acids or viruses, closely related substances such as microheterogeneous structural variants of the product, and reagents or aggregates. To achieve resolution it may be necessary to sacrifice sample load or even recovery (by peak cutting). 

In principle, the crystallization of a protein, nucleic acid, or virus (as exemplified in Figure 2.2) is little different than the crystallization of conventional small molecules. Crystallization requires the gradual creation of a supersaturated solution of the macromolecule followed by spontaneous formation of crystal growth centers or nuclei. Once growth has commenced, emphasis shifts to maintenance of virtually invariant conditions so as to sustain continued ordered addition of single molecules, or perhaps ordered aggregates, to surfaces of the developing crystal. 

The role of bioreceptor can be also played by viruses covalently attached to the electrode surface, which was shown for resistance detection of antibody and prostate-specific membrane antigen.135 Taking into account up to 1020 unique species, phage-displayed libraries provide a vast pool of candidate receptors to practically any analyte, including small molecules, proteins and nucleic acids. Piezoelectric virus sensor has been developed e.g. for detection of distinctive antigens of the human cytomegalovirus.136... 

Finally, another potential interplay between UVR and viruses occurs when they coexist with their host in a type of mutualistic relationship, where the nucleic acid of the virus is integrated in the genome of the host and is replicated with it (lysogenic state). Ultraviolet C radiation produced by germicidal lamps (max. at 254 nm) has normally been used, among other stressors, to induce the shift from lysogenic to lytic state in a complex mechanism involving the DNA repair SOS system of the host [93]. However, natural or simulated solar UVR seems not to be very efficient in this process [94,95]. 

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