Nucleic acid bases chemical reactions

A series of new amino acid derivatives having pendant nucleic acid bases was prepared by the reaction of L-lysine and L-glutamic acid with the nucleic acid bases. These amino acids were further polymerized by using the N-carboxyamino acid anhydride ( NCA ) method. Alternatively, the nucleic acid base substituted poly-L-lysines were also prepared by using polymer reactions which include the reaction of carboxyethyl derivatives of the bases onto poly-L-lysine. Physico-chemical properties of the polymers obtained were given. 

A new dimension in the development of nucleic acid based catalysts was introduced by Breaker and Joyce in 1994 when they isolated the first deoxyribozyme [111]. It is not unexpected that DNA is also able to catalyze chemical reactions because it was shown previously that ssDNA aptamers which bind to a variety of ligands can be isolated by in vitro selection [141]. In the meantime, several deoxyribozymes have been described which expand the range of chemical transformations accelerated by nucleic acid catalysts even further and raising question whether even catalytic DNA might have played some role in the pre-biotic evolution of hfe on earth [69-71]. 

As far as quantitative chemical derivatization GC analysis is concerned, it is necessary to mention especially the work of Gehrke and his collaborators, who specified the fundamental concepts of quantitative GC analysis combined with the chemical derivatization of sample compounds and applied them to the accurate determination of the twenty natural protein amino acids and other non-protein amino acids as their N-TFA-n-butyl esters [5 ], the urinary excretion level of methylated nucleic acid bases as their TMS derivatives [6], TMS nucleosides [7] and other investigations. Further examples include a computer program for processing the quantitative GC data obtained for seventeen triglyceride fatty acids after their transesterification by 2 NKOH in n-butanol [8], a study of the kinetics of the transesterification reactions of dimethyl terephthalate with ethylene glycol [9] and the GC-MS determination of chlorophenols in spent bleach liquors after isolation of the chlorophenols by a multi-step extraction, purification of the final extract by HPLC and derivatization with diazoethane [10]. 

A new departure in the development of nucleic acid based catalysts was made three years ago by Breaker and Joyce, who reported the isolation of the first deoxyribozyme. The proof that DNA can also catalyze chemical reactions is not completely unexpected, especially since it was shown shortly after the development of the in vitro selection technique that single-stranded DNA molecules can also be selected to bind to a variety of ligands. Meanwhile, several catalytically active DNAs have been described, expanding the range of nucleic acid catalyzed reactions even further. 

As mentioned above, once freed from the constraints of a complementary strand, polynucleotides can fold into a wide range of three-dimensional structures, leading to a diverse array of functions. Two specific types of functional polynucleotides are (1) aptamers, which bind noncovalently but selectively to ligands and (2) enzymes, which catalyze chemical reactions similar to protein enzymes. While a few examples of both natural aptamers and enzymes have been discovered, far more have been identified from synthetic combinatorial libraries through in vitro selection methods. The general approach to selection of functional polynucleotides is described below, followed by specific examples of nucleic acid-based aptamers and enzymes. 

Two other types of molecular database are pertinent to drug discovery. One is the so-called reaction database. It is a 2D database containing the reagents, products, and conditions of chemical reactions. The medicinal chemist would use one of these databases as a resource to find synthetic procedures. Another type of molecular database used in pharmaceutical and biotechnology research contains peptide sequences of proteins and nucleic acid base sequences of DNA and RNA. These sequence databases are essential in biotechnology and genomics, which have their role in modem dmg discovery. 

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... 

The more successful strategy for the isolation of RNA- and DNA-based catalysts involves the direct screening of nucleic acids libraries for catalytic activity. This approach is called direct selection [6, 65, 77, 78, 86, 101-107]. In direct selections, nucleic acids that are capable of catalyzing a particular chemical transformation modify themselves with a tag or other characteristic that allows their preferential enrichment over those molecules which are catalytically inactive [108]. The design of ribozyme-selections involving reactions between two small substrates requires that one reactant be covalently attached to every individual member of the starting RNA pool. After the reaction with another substrate which usually carries the selection-tag has occurred, the self-modified RNA is immobilized on a solid support, separated from non-active molecules, and then cleaved off the support. 

The terminology nucleotide or nucleoside immediately directs our thoughts towards nucleic acids. Remarkably, nucleosides and nucleotides play other roles in biochemical reactions that are no less important than their function as part of nucleic acids. We also encounter more stmctural diversity. It is rare that the chemical and biochemical reactivities of these derivatives relate specihcally to the base plus sugar part of the structure, and usually reside elsewhere in the molecule. Almost certainly, it is this base plus sugar part of the structure that provides a recognition... 

The purines and pyrimidines are relatively stable compounds with considerable aromatic character. Nevertheless, they react with many different reagents and, under some relatively mild conditions, can be completely degraded to smaller molecules. The chemistry of these reactions is complex and is made more so by the fact that a reaction at one site on the ring may enhance the reactivity at other sites. The reactions of nucleic acids are largely the same as those of the individual nucleosides or nucleotides, the rates of reaction are often influenced by the position in the polynucleotide chain and by whether the nucleic acid is single or double stranded. The reactions of nucleosides and nucleotides are best understood in terms of the electronic properties of the various positions in the bases.26 33 Most of the chemical reactions are nucleophilic addition or displacement reactions of types that are discussed in Chapters 12 and 13. 

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