Nucleic acids, literature reviews

This year s nucleotide and nucleic acid literature has been dominated by interest in internucleoside linkages. A number of approaches to novel internucleoside linkages in dimers have been published in addition to stereoselective routes to phosphorothioate and methylphosphonate linkages. In some cases these studies have also extended to the oligonucleotide level. In addition a number of novel nucleotide analogues have been described. One of the most exciting areas in the field of nucleic acid chemistry is the application of in vitro selection techniques and these are reviewed for the first time. 

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. 

This series in heterocyclic chemistry is being introduced to collectively make available critically and comprehensively reviewed literature scattered in various journals as papers and review articles. All sorts of heterocyclic compounds originating from synthesis, natural products, marine products, insects, etc. will be covered. Several heterocyclic compounds play a significant role in maintaining life. Blood constituent hemoglobin and purines as well as pyrimidines, are constituents of nucleic acid (DNA and RNA) are also heterocyclic compounds. Several amino acids, carbohydrates, vitamins, alkaloids, antibiotics, etc. are also heterocyclic compounds that are essential for life. Heterocyclic compounds are widely used in clinical practice as drugs, but all applications of heterocyclic medicines can not be discussed in detail. In addition to such applications, heterocyclic compounds also find several applications in the plastics industry, in photography as sensitizers and developers, and in dye industry as dyes, etc. 

The reader is referred to other reviews for detailed discussions of the electronic states and luminescence of nucleic acids and their constituents/0 fluorescence correlation spectroscopy/2) spectroscopy of dye/DNA complexes/0 and ethidium fluorescence assays/4,0 A brief review of early work on DNA dynamics as well as a review of tRNA kinetics and dynamics have also appeared. The diverse and voluminous literature on the use of fluorescence techniques to assay the binding of proteins and antitumor drugs to nucleic acids and on the use of fluorescent DNA/dye complexes in cytometry and cytochemistry lies entirely outside the scope of this chapter. 

The concept of the similarity of molecules has important ramifications for physical, chemical, and biological systems. Grunwald (7) has recently pointed out the constraints of molecular similarity on linear free energy relations and observed that Their accuracy depends upon the quality of the molecular similarity. The use of quantitative structure-activity relationships (2-6) is based on the assumption that similar molecules have similar properties. Herein we present a general and rigorous definition of molecular structural similarity. Previous research in this field has usually been concerned with sequence comparisons of macromolecules, primarily proteins and nucleic acids (7-9). In addition, there have appeared a number of ad hoc definitions of molecular similarity (10-15), many of which are subsumed in the present work. Difficulties associated with attempting to obtain precise numerical indices for qualitative molecular structural concepts have already been extensively discussed in the literature and will not be reviewed here. 

Discussion in this section is confined to the matter mentioned in the introduction, which has provided such a fresh and energetic impetus to this whole subject, namely the direct and quantitative correlation between the amounts of several specific and identifiable photoproducts formed in the photolysis of nucleic acids and the amount of inactivation of the nucleic acid biological function. This specific area, however, is one which has drawn much attention, and to which several of the recent reviews are devoted.8,10,113"90 There is little need to extend these excellent articles, and so a comprehensive survey of the literature will not be attempted here, but merely a summary and interpretation. 

In the various reviews on self-reproduction in recent years, practically no mention is made of such micelles or vesicle systems. The reason lies most prohahly in the bias of classic hiochemical literature, according to which self-replication is tantamount to nucleic acid systems lacking this are therefore deemed not to he relevant. In this particular regard, it is argued that self-reproduction of micelles and vesicles proceeds without transmission of information. 

The universal character of the LbL method has catalyzed the introduction of the method for a wide range of bioapplications. Proteins (enzymes) [30-33], polypeptides [34], polysaccharides [35], lipids [36, 37], nucleic acids [38-42], viruses [43], inorganic particles, and crystals [44] have been embedded in the films. Use of these compounds makes the films attractive for biorelated applications such as biosensors, drug delivery, tissue engineering, and biocoatings. Biological [45, 46] and nonbio-logical [21, 47 19] applications of LbL films are reviewed in the literature. 

The knowledge of the chemistry and structure of nucleic acids as well as their metabolic and catabolic pathways has been extensively increased. However, there is very little evidence about the role of transition elements in the biochemistry of nucleic acids. Therefore, this review should emphasize the present status of the literature about studies of transition metal interactions with the monomer and polymer units of nucleic acids. Although this survey is far from being comprehensive it is hoped that the data collected here will be helpful for further investigations on the biochemical behavior of transition metals in nucleic acid metabolism. 

In 1980-1982 comprehensive reviews on Raman and resonance Raman studies of biological and biochemical systems appeared in the literature (Carey and Solares, 1980 Carey, 1982). Particularly work on protein conformation, natural, protein-bound chro-mophores, resonance Raman labels (as already mentioned above), nucleic acids and nucleic acid-protein complexes as well as on lipids, membranes, and carbohydrates were reviewed. 

The importance to science of the nucleic acids has currently reached awesome proportions and the literature is now very substantial indeed. It is therefore beyond the scope of this article to give more than the briefest mention of purine nucleoside, nucleotide and nucleic acid chemistry. However, Table 2 lists some useful reviews on the subject. 

The Af-glycosylpurines or purine nucleosides include many naturally occurring compounds, especially 9-/3-D-ribofuranosyl and 9-/3-D-2-deoxyribofuranosyl derivatives of adenine and guanine which are of course major constituents of the various ribo (RNA) and deoxyribo (DNA) nucleic acids. The literature on purine nucleoside chemistry is very substantial and in this chapter it will only be possible to give a brief survey. However several reviews exist (see Table 2). 

---