Chemical nucleic acids

In this book, we concentrate largely on methods for the computer manipulation of small and medium-sized molecules, molecules of up to a few hundred or thousand atoms. We do this to develop an understanding of the methods available for the processing of information on chemical compounds and reactions. However, many of these methods can also be applied to macromolecules such as proteins and nucleic acids. 

Cornell W D, P Cieplak, CI Bayly, I R Gould, K M Merz Jr, D M Ferguson, D C Spellmeyer, T Fox, J W Caldwell and P A Kollman 1995. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules. Journal of the American Chemical Society 117 5179-5197. 

Much effort has been placed in the synthesis of compounds possessing a chiral center at the phosphoms atom, particularly three- and four-coordinate compounds such as tertiary phosphines, phosphine oxides, phosphonates, phosphinates, and phosphate esters (11). Some enantiomers are known to exhibit a variety of biological activities and are therefore of interest Oas agricultural chemicals, pharmaceuticals (qv), etc. Homochiral bisphosphines are commonly used in catalytic asymmetric syntheses providing good enantioselectivities (see also Nucleic acids). Excellent reviews of low coordinate (coordination numbers 1 and 2) phosphoms compounds are available (12). 

Standardization and Testing". The Center for Biologies Evaluation and Research has set guidelines for the vaccine which include standards for si2e of the individual polysaccharides and specifications for both purity (absence of protein and nucleic acid) and chemical and immunological identity. 

Nucleic acids are the molecules of the genetic apparatus. They direct protein biosynthesis in the body and are the raw materials of genetic technology (see Genetic engineering). Most often polynucleotides are synthesized microbiologicaHy, or at least enzymatically, but chemical synthesis is possible. 

This chapter lists some representative examples of biochemicals and their origins, a brief indication of key techniques used in their purification, and literature references where further details may be found. Simpler low molecular weight compounds, particularly those that may have been prepared by chemical syntheses, e.g. acetic acid, glycine, will be found in Chapter 4. Only a small number of enzymes and proteins are included because of space limitations. The purification of some of the ones that have been included has been described only briefly. The reader is referred to comprehensive texts such as the Methods Enzymol (Academic Press) series which currently runs to more than 344 volumes and The Enzymes (3rd Edn, Academic Press) which runs to 22 volumes for methods of preparation and purification of proteins and enzymes. Leading referenees on proteins will be found in Advances in Protein Chemistry (59 volumes. Academic Press) and on enzymes will be found in Advances in Enzymology (72 volumes, then became Advances in Enzymology and Related Area of Molecular Biology, J Wiley Sons). The Annual Review of Biochemistry (Annual Review Inc. Patio Alto California) also is an excellent source of key references to the up-to-date information on known and new natural compounds, from small molecules, e.g. enzyme cofactors to proteins and nucleic acids. 

Nucleic acids in the DNA contain a high number of nucleophilic sites that can be attacked by electrophilic intermediates (metabolites) of chemical compounds. DNA adducts formed may cause alterations in the expression of a critical gene in the cell and thus lead to cell death. For example, modification of p53 tumor suppressor gene may inactivate the functions of the p53 protein and render cells sensitive to malignant transformation. Also, formation of RNA adducts may inhibit key cellular events because RNA is essential for protein synthesis. 

Several chemical compounds may cause inflammation or constriction of the blood vessel wall (vasoconstriction). Ergot alkaloids at high doses cause constriction and thickening of the vessel wall. Allylamine may also induce constriction of coronary arteries, thickening of their smooth muscle walls, and a disease state that corresponds to coronary heart disease. The culprit is a toxic reactive metabolite of allylamine, acrolein, that binds covalently to nucleophilic groups of proteins and nucleic acids in the cardiac myocytes. 

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