Subject Nucleic acid

Some aspects, such as the computer representation and manipulation of proteins and nucleic acids, could not be covered. Even the modeling of the interactions of small molecules with proteins, as dealt with in docking software or software for de novo design could not be included in the Textbook, although chapters in the Handbook do treat these subjects. 

Polymers of amino acids, like polymers of nucleic acids, have both ionic and hydrophobic character. Unlike the polymers of nucleic acids, amino acid polymers may carry either a negative or a positive (or zero) net charge, are far more subject to irreversible denaturation and oxidation, and are labile to... 

The prebiotic chemistry of the nucleic acid bases is still the subject of debate among experts. One of the most mindful critics is Robert Shapiro, professor of chemistry at New York University and a DNA expert. His book Origins-A Sceptic s Guide to Creation of Life on Earth includes a critical analysis of the results previously obtained in biogenesis research (Shapiro 1986). Shapiro s has been the critical voice in the community of biogenesis researchers for many years. He identifies the weak points in some of the audacious hypotheses, which are often raised to the status of theories even though they involve many open questions. 

The minimal cell, as the simplest system which has all the required properties of life (metabolism, self-reproduction and the ability to evolve), is presently studied as part of a new research discipline synthetic biology. This includes subjects such as synthesis in branches of biological systems, for example, of new RNA species, new peptides and new nucleic acid analogues, as well as the synthesis of peptide nucleic acids. One example is the work of M. R. Ghadiri and G. von Kiedrowski on self-replication of oligonucleotides and oligopeptides (Luisi, 2006b). 

The components of nucleic acids have been the subject of continuous DFT stud-ies61 S5,67 69. Jasien and Fitzgerald calculated dipole moments and polarizabilities for a series of molecules of biological interest including nucleic acid bases (adenine, thymine, cytosine, and guanine) and their pairs (adenine-thymine and cytosine-guanine)61. A good correlation between DFT(HL), experimental, and MP2 results was obtained for dipole moments and polarizabilities. More detailed analyses of DFT(SVWN) and DFT(B88/P86) results, which included vibrational frequencies, were reported for isolated bases and their... 

The next step was identification and isolation of DNA fragments encoding the biocatalyst. The same procedure can be applied to any active microorganism. DNA plasmid (Plasmid pTOXI-1 and Plasmid pTOXI-2) and vectors (four different nucleic acid sequences were included, namely SEQ ID No. 1 to 4 see original reference for details [38]) were constructed based on the identified and isolated fragments and constitute part of the claimed subject matter. The described expression of the Dsz+ trait in both a related and non-related heterologous host detailed in the patent, seems to indicate that pTOXI-1 (see patent document [38]) carries all of the genetic information required for conversion of DBT to 2-HBP. 

Nucleic acids, DNA and RNA, are attractive biopolymers that can be used for biomedical applications [175,176], nanostructure fabrication [177,178], computing [179,180], and materials for electron-conduction [181,182]. Immobilization of DNA and RNA in well-defined nanostructures would be one of the most unique subjects in current nanotechnology. Unfortunately, a silica surface cannot usually adsorb duplex DNA in aqueous solution due to the electrostatic repulsion between the silica surface and polyanionic DNA. However, Fujiwara et al. recently found that duplex DNA in protonated phosphoric acid form can adsorb on mesoporous silicates, even in low-salt aqueous solution [183]. The DNA adsorption behavior depended much on the pore size of the mesoporous silica. Plausible models of DNA accommodation in mesopore silica channels are depicted in Figure 4.20. Inclusion of duplex DNA in mesoporous silicates with larger pores, around 3.8 nm diameter, would be accompanied by the formation of four water monolayers on the silica surface of the mesoporous inner channel (Figure 4.20A), where sufficient quantities of Si—OH groups remained after solvent extraction of the template (not by calcination). 

Accordingly, the contribution of this metabolic activation pathway to the formation of covalently-bound adducts of arylamides with cellular proteins and nucleic acids has been the subject of numerous investigations, and has been reviewed extensively by Mulder (25). From these and more recent data (4,26,27) it is apparent, particularly in the case of N-hydroxy-AAF Tn-OH-AAF), that in vivo formation of reactive N-sulfonyloxy derivatives is primarily... 

Since the chemistry of nucleic acids was last discussed in this Series,1 publications on the subject have appeared at an unprecedented rate. Degradation products have been further investigated and their structures are more firmly established. Moreover, studies of the properties of these materials have led to a fuller understanding of the behavior of polynucleotides. Emphasis will be laid on the organic chemistry of nucleic acids, and many physicochemical investigations will not be discussed. The period under review has seen the beginning of an understanding of the biosynthesis of nucleic acids, but space does not allow of a consideration of this aspect of the subject. 

Biophysical analysis of biomolecules like proteins, nucleic acids, or lipids utilizes intrinsic physical properties of the observed molecule itself or of an associated reporter molecule, which reflect information about structural characteristics, interactions, or reactions of the subject observed. In most cases the analysis (and the labels introduced) only interferes slightly with the interaction of interest and does not induce significant changes in the properties of the reactants. 

The chemistry, metabolism, and clinical importance of folic acid have been the subject of many excellent reviews (A7, Gil, H14, H20, Rl). Folic acid deficiency leads to a macrocytic anemia and leucopenia. These symptoms are due to inadequate synthesis of nucleic acid. The synthesis of purine bases and of thymine, required for nucleic acid synthesis, is impaired in folic acid deficiency. Detection of folic acid activity in biologic fluids and tissues is of the utmost importance it distinguishes between the various anemias, e.g., those due to vitamin Bi2 or folic acid deficiency. Because morphology of the abnormal red cell does not help in diagnosing vitamin deficiency, one must rely on assay methods for differential diagnosis. Treatment of pernicious anemia with folic acid has led to subacute combined degeneration of the spinal cord despite... 

Yamane T, Davidson N (1962) On the complexing of deoxyribonucleic acid by silver . Biochim Biophys Acta (BBA) 55 609-621, Specialized section on nucleic acids and related subjects... 

Much of the information has been updated for the second edition to reflect substantial changes in the subject. The edition of a chapter on nucleic acids was considered essential and complements the original chapters on the chemical nature and methods of analysis of other important biological molecules. We are indebted to Dr Susan Laird for compiling this chapter and also to Mr Robert Smith for the major update on immunoassays in the immunological methods chapter. 

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