Nucleic acid bases, nucleosides and nucleotides

Wyard SJ, Elliott JP (1973) ESR studies of radiation damage in nucleic acids, bases, nucleosides and nucleotides. Ann NY Acad Sci 222 628-639... 

Preparation of the TMS derivatives of nucleic acid bases, nucleosides and nucleotides [251] After thoroughly drying the sample overnight in a vacuum desiccator in the presence of P2O5, transfer a 50 pg portion to a suitable reaction vial, and add BSTFA containing 1% TMCS (40/il) and pyridine (10/il). Heat the tightly capped reaction vial at 100 °C for ih. After cooling to room temperature the reaction mixture can be... 

Boron nucleic acid bases, nucleosides and nucleotides 12MR0418. Chemical synthesis of nucleoside analogues 13MI19. 5-Hydroxymethylcytosine The elusive epigenetic mark in mammalian DNA 12CSR6916. 

Raaen, H. P., and Kraus, F. E. (1968). Resolution of complex mixtures of nucleic acid bases, nucleosides and nucleotides by two-dimensional thin layer chromatography on polyethyleneimine-cellulose. J. Chromatogr. 35 531-537. 

PEI-cellulose has been extensively studied and used in the separation of nucleic acid bases, nucleosides, and nucleotides, with good separation and resolution. It is also used for the separation of RNA and DNA hydrolysates, and large scale preparations among other applications. We feel this remains the most versatile layer for separations of dNMPs. 

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... 

A wide variety of bases, nucleosides and nucleotides have been separated using porous layer bead ion exchangers. A representative chromatogram of the separation of ribonucleoside mono-phosphoric acids from the work of Smukler ( ) is shown in Figure 4. Recently, ion exchangers chemically bonded to small particle diameter (> 10 ym) silica have been successfully applied to the separation of nucleic acid constitutents (37). The rapid separations using such supports undoubtedly mean that they will find increasing use in the future. 

Bases, Nucleosides, and Nucleotides. The relationship of these components of a nucleic acid or polynucleotide is shown in Chart 10. The numbering of the pyrimidine (uracil) and the purine (adenine) shown is the IUPAC nomenclature used by Chemical Abstracts, and... 

Johnson, J. Am. Chem. Soc. 55, 1733 (1933). From d-meth-ylmalic acid Scherp, J. Am. Chem. Soc. 68, 912 ((946). Crystal structure of monohydrate Gerdit. Acta Cryst. 14, 333 (1961). Review Ts o, Bases. Nucleosides and Nucleotides in Basic Principles in Nucleic Acid Chemistry vol. 1, P. O, P. Ts o, Ed, (Academic Press, New York, 1974) pp 453-584. See also Nucleic Acids. 

Immobilized nucleic acid bases, nucleosides or oligonucleotides may be used for separation, fractionation and structure determination of various nucleic acids and enzymes participating in their synthesis and degradation. Schott et al. [139,229] made use of immobilized defined oligonucleotides for the selective separation of free nucleotides on the basis of a base-pairing mechanism. Complementary oligonucleotides in the mobile phase are selectively adsorbed on the immobilized template if... 

Nucleic nitrogen is present in purine and pyrimidine bases, nucleosides and nucleotides, as well as nucleic acids. This form of nitrogen has not been extensively studied. 

Pataki, G., and Niederwieser, A. (1967). Thin-layer chromatography of nucleic acid bases, nucleosides, nucleotides and related compounds. IV. Separation on PEI-cellulose layers using gradient elution and direct fluorometry of spots. J. Chromatogr. 29 133-141. 

Nucleotides are the basic building blocks of nucleic acids, whereas nucleosides are nucleotides without the phosphate group (i.e., nucleoside = base + sugar, and nucleotide = base + sugar + phosphate). 

Excess ultrasonic absorptions due to protolysis and hydrolysis have also been observed for a variety of bases, nucleosides and nucleotides (38a). These proton transfers involve the secondary phosphoric acid function of nucleotides and/or functional groups or aromatic nitrogen atoms in bases and nucleosides. The latter are also observed with nucleic acids (38c). 

In contrast to Mg + and Mn +, which stabilize secondary structures in DNA and RNA, Cu + destabilizes DNA and RNA double helices, and this is attributed to the ability of copper to bind to the nucleic acid bases. Chao and Kearns have recently explored the possibility that this binding, as detected by electron and nuclear magnetic resonance spectroscopy, might be used to probe certain structural features of nucleic acid molecules, such as the looped out regions of tRNAs. The nature of the Cu complexes formed with nucleosides and nucleotides varies with the specific nucleic acid derivatives used and also the pH. Thus, in the pH range 8.5—10.0, copper forms a water-soluble complex with the ribose OH groups of the ribonu-cleosides and 5 -ribonucleotides, but these complexes cannot form with any of the deoxynucleosides or the 2 - and 3 -ribonucleotides. It is suggested that copper(ii) could stabilize unusual polynucleotide structures or interactions in certain enzymatic systems the latter could, for example, be responsible for translational errors in the RNA,DNA polymerase system which are known to be induced by transition metals. 

Another naturally occurring sugar in nucleosides is arabi-nose. The arabinosides inhibit many nucleic acid enzymes and have widespread therapeutical applications. Some bases, nucleosides, and nucleotides, with indications of their protonation sites, are listed in Fig. 3.1. The abbreviations used are found in the Appendix. 

J. -L. Imbach, Systematic synthesis and antiviral evaluation of a-L-arabinofuranosyl and 2 -deoxy-a-L-erythro-pentofwrsinosyl nucleosides of the five naturallly occurring nucleic acid bases, Nucleosides Nucleotides 10 1345 (1991). 

All the nucleic acid bases absorb UV radiation, as seen in Tables 11-1, 11-2, 11-3, 11-4, and 11-5, making them vulnerable to the UV radiation of sunlight, since the energy of the photons absorbed could lead to photochemical reactions. As already mentioned above, the excited state lifetimes of the natural nucleobases, and their nucleotides, and nucleosides are very short, indicating that ultrafast radiationless decay to the ground state takes place [6], The mechanism for nonradiative decay in all the nucleobases has been investigated with quantum mechanical methods. Below we summarize these studies for each base and make an effort to find common mechanisms if they exist. 

Phenylglyoxal and alkoxyphenylglyoxals react selectively with the guanine moiety of nucleosides and nucleotides in phosphate buffer (pH 7.0) at 37°C for 5-7 min to give the corresponding fluorescent derivatives [12-15], as shown in Figure 6. Other nucleic acid bases and nucleotides (e.g., adenine, cytosine, uracil, thymine, AMP, CMP) do not produce derivatives under such mild reaction conditions. The fluorescent derivative emits chemiluminescence on oxidation with di-methylformamide (DMF) and H202 at pH 8.0-12 [14, 15],... 

The obvious similarity between the purine bases of DNA and pteridines, especially between guanosine and pterins, has encouraged extensive studies of the synthesis and properties of pteridine-containing nucleoside and nucleotides. Synthetic methods have naturally built upon established methods of nucleic acid synthesis. The primary property of use in applications of these compounds to DNA chemistry is fluorescence, which is very much greater for pteridines than for purines. 

Cytosine, thymine, and uracil are pyrimidines along with adenine and guanine they account for the five nucleic acid bases. Pyrimidines are heterocyclic single-ringed compounds based on the structure of pyrimidine. Cytosine, thymine, and uracil, like adenine and guanine, form nucleosides and nucleotides in RNA and DNA. When the bases combine with ribose, a ribo-nucleoside forms and when it attaches to deoxyribose, a deoxyribosenucleoside is formed. Names of the nucleoside are summarized in Table 29.1. These in turn combine with phospho-ryl groups, in a process called phosphorylation, to form their respective nucleotides that form nucleic acids. The nucleotides can be tri, di, and mono phosphate nucleotides similar to the way in which adenine forms ATP, ADP, and AMP. 

The study of the nucleic acid bases is interesting because they possess many possible sites of protonation or electrophilic attack. Isopotential maps have been constructed for adenine, cytosine, and thymine.244 They may be used to study theoretically the proton affinities of the different atoms in these molecules. It is well known that protonation of cytosine, its nucleotide or nucleoside, occurs at N-394,245-247 (cf. Section II) alkylation also occurs at N-3.103-248-249 Nevertheless protonation of the oxygen of cytosine in DNA has been reported.250 The basic pA of cytosine is higher than that of adenine. The isopotential map in the molecular plane of cytosine (Tig. 8) shows that the potential well is deeper for N-3 than for 0 and the minimum for N-3 in cytosine is deeper than for any nitrogen in adenine. These maps, and their confrontation with the experimental facts have been discussed228-244... 

The nucleoside formed from hypoxanthine and ribose is known as inosine (Ino or I) and the corresponding nucleotide as inosinic acid. Further substitution at C-2 of -H by -OH and tautomerization yields xanthine (Xan). Its nucleoside is xanthosine (Xao, X). A similar hydroxylation at C-7 converts xanthine to uric acid, an important human urinary excretion product derived from nucleic acid bases. 

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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