Nuclear /nucleic

The supernatant contains cytoplasmic nucleic acids and proteins, and extraction of the nucleic acids can be accomplished with phenol (see below). This preparation does not entirely purify cytoplasmic nucleic acids, as some nuclear nucleic acids are also isolated. In our... 

The problem of non-RNA organic phosphorus compounds as contaminants in the RNA fraction has been studied by Mauritzen and Stedman (75) in connection with their RNA analyses of isolated cell nuclei, where this constituent is present in very small quantities. They present extensive data concerning the degree of contamination of the RNA nucleotides with organic and inorganic phosphates following the alkaline d estion, in the ST or STS procedure, of nuclear nucleic acids. They concluded that, for accurate assay of RNA in these methods, it is necessary to convert the pentose in the RNA fraction to furfural (5,33) with acid digestion, and assay the distilled furfural by the formation of a colored product with aniline acetate. Similar data on this type of contamination of various tissue fractions is presented by Davidson and Smellie (32) (see Section II, 1, F). 

Zinc. The 2—3 g of zinc in the human body are widely distributed in every tissue and tissue duid (90—92). About 90 wt % is in muscle and bone unusually high concentrations are in the choroid of the eye and in the prostate gland (93). Almost all of the zinc in the blood is associated with carbonic anhydrase in the erythrocytes (94). Zinc is concentrated in nucleic acids (90), and found in the nuclear, mitochondrial, and supernatant fractions of all cells. 

Technetium-99m coordination compounds are used very widely as noniavasive imaging tools (35) (see Imaging technology Radioactive tracers). Different coordination species concentrate ia different organs. Several of the [Tc O(chelate)2] types have been used. In fact, the large majority of nuclear medicine scans ia the United States are of technetium-99m complexes. Moreover, chiral transition-metal complexes have been used to probe nucleic acid stmcture (see Nucleic acids). For example, the two chiral isomers of tris(1,10-phenanthroline)mthenium (IT) [24162-09-2] (14) iateract differentiy with DNA. These compounds are enantioselective and provide an addition tool for DNA stmctural iaterpretation (36). 

Clore, G.M., Gronenborn, A.M. Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magetic resonance spectroscopy. CRC Crit. Rev. Biochem. 24 479-564, 1989. 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Virus maturation and assembly at the cell membrane or the nuclear membrane has long been seen as a potential target for antiviral compounds. For the virus to mature and be released in a conformation that will insure stability and survival of the viral genome in the exttacellular enviromnent, the protein subunits of the capsid or nucle-ocapsids have to be transported to the assembly point where they will form the final particles around the viral nucleic acid. If this process does not occur in an orderly and programmed manner, the capsid subunits will not form the required multimers and the viral components will become targets for the cellular disposal mechanisms. 

Sazani P., Kang S.H., Maier M.A., Wei C., Dillman j., Summerton J., Mano-haran M., Kole R. Nuclear antisense ef fects of neutral, anionic and cationic oligonucleotide analogs. Nucleic Acids Res. 2001 29 3965-3974. 

Boffa L.C., Scarf S., Marian M.R., Dai40nte G, Allfrey V.G., Benatti U., Morris O. L. Dihydrotestosterone as a selective cellular/nuclear localization vector for anti-gene peptide nucleic acid in prostatic carcinoma cells. Cancer Res. 2000 60 2258-2262. 

Braun K., Peschke P., Pipkorn R., Lam-pel S., Wachsmuth M., Waldeck W., Friedrich E., Debus J. A biological transporter for the delivery of peptide nucleic acids (PNAs) to the nuclear compartment of living cells./. Mol. Biol. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

The refinement of other analytical methods, such as electrophoresis [34,36], the various techniques of optical spectroscopy [103-105], and nuclear magnetic resonance [201], is supplemented by the recent advances in real-time affinity measurements [152,202], contributing to the understanding of biomolecular reactivity. Taken together, the improvement of analytical methods will eventually allow a comprehensive characterization of the structure, topology, and properties of the nucleic acid-based supramolecular components under consideration for distinctive applications in nanobiotechnology. 

Feigon J, Koshlap KM, Smith FW (1995) Methods Enzymol Nuclear Magn Reson Nucleic Acids 261 225... 

Not all the cellular DNA is in the nucleus some is found in the mitochondria. In addition, mitochondria contain RNA as well as several enzymes used for protein synthesis. Interestingly, mitochond-rial RNA and DNA bear a closer resemblance to the nucleic acid of bacterial cells than they do to animal cells. For example, the rather small DNA molecule of the mitochondrion is circular and does not form nucleosomes. Its information is contained in approximately 16,500 nucleotides that func-tion in the synthesis of two ribosomal and 22 transfer RNAs (tRNAs). In addition, mitochondrial DNA codes for the synthesis of 13 proteins, all components of the respiratory chain and the oxidative phosphorylation system. Still, mitochondrial DNA does not contain sufficient information for the synthesis of all mitochondrial proteins most are coded by nuclear genes. Most mitochondrial proteins are synthesized in the cytosol from nuclear-derived messenger RNAs (mRNAs) and then transported into the mito-chondria, where they contribute to both the structural and the functional elements of this organelle. Because mitochondria are inherited cytoplasmically, an individual does not necessarily receive mitochondrial nucleic acid equally from each parent. In fact, mito-chondria are inherited maternally. 

Volume 261. Nuclear Magnetic Resonance and Nucleic Acids... 

Rozen, F., and Sonenberg, N. (1987). Identification of nuclear cap specific proteins in HeLa cells. Nucleic Acids Res. 15, 6489-6500. 

In general, the mechanism of heat and alkaline solution for DNA extraction may be based upon a hypothesis, previously proposed for the AR technique.32 Strong alkaline solution may denature and hydrolyze proteins, resulting in breaking cell and nuclear membranes as well as disrupting cross-linkages due to formalin fixation. It is no surprise to observe the similarity between retrieval of nucleic acid and retrieval of protein (antigen) based on a similar chemical reaction of formaldehyde with these two kinds of macromolecules (Fig. 3.1).15"19... 

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