Nucleic acids entries

FIGURE 1.25 The virus life cycle. Viruses are mobile bits of genetic iuformatiou encapsulated in a protein coat. The genetic material can be either DNA or RNA. Once this genetic material gains entry to its host cell, it takes over the host machinery for macromolecular synthesis and subverts it to the synthesis of viral-specific nucleic acids and proteins. These virus components are then assembled into mature virus particles that are released from the cell. Often, this parasitic cycle of virus infection leads to cell death and disease. 

Genetic informahon for viral reproduchon resides in its nucleic acid (DNA or RNA see Chapter 3). The viral particle (virion) does not possess enzymes necessary for its own replication after entry into the host cell, the vims uses the enzymes already present or induces the formahon of new ones. Vimses replicate by synthesis of their separate components followed by assembly. 

Selected entries from Methods in Enzymology [vol, page(s)] Anisotropy effects, 261, 427-430 determination by dynamic laser light scattering (quasi-elastic light scattering), 261, 432-433 determination for nucleic acids by NMR [accuracy, 261, 432-433 algorithms, 261, 11-13, 425, 430 carbon-13 relaxation, 261, 11-12, 422-426, 431, 434-435 cross-relaxation rates, 261,419-422, 435 error sources, 261, 430-432 phosphorus-31 relaxation, 261, 426-427, 431 proton relaxation, 261,51,418-422 relaxation matrix calculations, 261,12] deuterium solvent viscosity effects, 261,433 effect... 

Selected entries from Methods in Enzymology [vol, page(s)] . Applications, 246, 335 [immunoassay, 246, 343-344 nucleic acids, 246, 344-345 photoreceptors, 246, 341-343 protein conformation, 246, 339-340 protein-membrane interactions, 246, 340-341 two-dimensional imaging, 246, 345] energy level diagram, 246, 336 excited state decay kinetics, 246, 337-338 in-... 

Chaurasia, G., Iqbal, Y., Hanig, C., Herzel, H., Wanker, E.E. and Futschik, M.E. (2007) Uniin An Entry Gate to the Human Protein Interactome. Nucleic Acids Res, 35, D590-594. 

Viral replication consists of several steps (Figure 49-1) (1) attachment of the vims to receptors on the host cell surface (2) entry of the virus through the host cell membrane (3) uncoating of viral nucleic acid (4) synthesis of early regulatory proteins, eg, nucleic acid polymerases (5) synthesis of new viral RNA or DNA (6) synthesis of late, structural proteins (7) assembly (maturation) of viral particles and (8) release from the cell. Antiviral agents can potentially target any of these steps. 

Both the nucleic acid sequences and the protein sequences derived from the biological information are collected in most such databases. Large amounts of data in these databases need to be sorted, stored, retrieved, and analyzed. Selection of subsets of data for particular analysis should also be done. IT providers designed such a data warehouse and developed an interface that provides an important benefit to researchers by making it easy to access the existing information and also to submit new entries (i.e., datamining) (Table 5.6). Middlewares and structured query language (SQL) softwares were developed for this purposes. The former one is used... 

A supported sulfide source has been demonstrated by Zhang et al.16 to synthesize oligonucleotide phosphorothioates (entry 12). Aminodithiazole-thione attached to a methacrylate-ethyleneglycol copolymer is used to efficiently convert a nucleotide phosphite to a phosphorothioate. The product nucleotide possesses protecting groups suitable for solid-phase oligonucleotide synthesis and thus is a valuable building block for nucleic acid therapeutics. 

Gene delivery into eukaryotic cells is commonly performed for research purposes as well as in gene therapy procedures. Cellular membranes do not spontaneously take up ectopic nucleic acid because of the polar nature of the phospholipid bilayer [1] which functions as a natural barrier that prevents entry of most water-soluble molecules such as nucleic acids. In studies of gene or protein function and regulation, manipulation of the intracellular expression level is a fundamental approach. For this reason, multiple methods for delivery of nucleic acids through membranes using chemical, physical, or biological systems have been established in the last 40 years. 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http //www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box query by PDB id only ) or keywords (check the box match exact word ) and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in. jpg or. gif image format. 

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