Nucleic acid bases, nucleosides and

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. 

DEGRADATION OF NUCLEIC ACIDS, NUCLEOTIDES, NUCLEOSIDES AND BASES THE GENERATION OF AMMONIA 217... 

Degradation of nucleic acids, nucleotides, nucleosides and bases the generation of ammonia... 

Figure 10.8 A summary of the reactions involved in the degradation of nucleic acid, nucleotides, nucleosides and purine and pyn midine bases. Nucleic add is hydrolysed by nucleases to form nucleotides, which are hydrolysed to nucleosides. The latter are split into ribose 1-phosphate and a base. The purine bases are converted to uric acid and ammonia. Uric acid is excreted. The pyrimidine bases are converted to 3-carbon intermediates (malo-nate semialdehyde and methylmalonate semialdehyde). The nitrogen is released as ammonia or used to convert oxoglutarate to glutamate.

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... 

Nucleic acids, nucleic acid bases, nucleotides and nucleosides... 

Fig. 10.28 The structures and literature references of nucleic acid bases, nucleotides and nucleosides that have been studied by INS spectroscopy.

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... 

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. 

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. 

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). 

It can be seen from the figure that the electrostatic repulsive forces between the macrocations are overwhelmed, probably by hydrophobic attractive forces between their hydrophobic side groups. It should be noted that the complimentary base-base pairing is unimportant in the present case. If this is not the case, the mixtures of APVP and TPVP should show the largest hypochromicity. This, however, is not the case. The importance of the hydrophobic interactions between nucleic acid bases has been proposed by Ts o et al.I9 from thermodynamic parameters of various nucleic acid bases or nucleosides in aqueous media. 

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. 

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],... 

Separation of proteins Separation of nucleosides Separation of nucleic acid bases and their nucleosides... 

Allen, D., and El Rassl, Z. (2004). Capillary electrochromatography with monolithic silica columns III. Preparation of hydrophilic silica monoliths having surface-bound cyano groups chromatographic characterization and application to the separation of carbohydrates, nucleosides, nucleic acid bases and other neutral polar species.. Chromatogr. A 1029, 239—247. 

Ohyama, K., Fujimoto, E., Wada, M., Kishikawa, N., Ohba, Y., Akiyama, S., Nakashima, K., and Kuroda, N. (2005). Investigation of a novel mixed-mode stationary phase for capillary electrochromatography. Part III separation of nucleosides and nucleic acid bases on sulfonated naphthalimido-modified silyl silica gel.. Sep. Sci. 28, 767—773. 

When a nucleic acid base is N-glycosidically linked to ribose or 2-deoxyribose (see p.38), it yields a nucleoside. The nucleoside adenosine (abbreviation A) is formed in this way from adenine and ribose, for example. The corresponding derivatives of the other bases are called guanosine (G), uridine (U), thymidine (T) and cytidine (C). When the sugar component is 2-deoxyribose, the product is a deoxyribonucleoside—e. g., 2 -deoxyadeno-... 

A series of the nucleic acid bases of the racemic 2 -deoxy-2, 3 -seco-nucleosides were prepared starting with l,3-dichloro-2-propanol, which was converted to 1160 and then to 1161. The condensation of the silylated bases... 

Addition of P F]F2 (or CH3C02f F]F) at the double bond of substituted 2,4-dioxypyrimidines (Scheme 16) allows the preparation of the fluorine-18-labelled nucleic acid base 5-[ F]fluorouracil [91-94] and the nucleoside 2 -deoxy-5-[ F]fluorouridine [95-97]. The reaction, usually carried out in acetic acid, demonstrates an excellent regioselectivity, with only the 5-[ F]fluoro derivatives obtained because the C-5 position is the unique activated position for reaction with an electrophile in these systems. The mechanism of this reaction has been studied and the intermediate 5,6-fluoro-acetoxy adduct (or the 5,6-fluoro-hydroxy adduct if the solvent is water) has been isolated and characterised [92]. 

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... 

Compounds based on the purine structure are classified as purines. Adenine is one of the two purines found in DNA and RNA. The other is guanine. Adenine and guanine are called bases in reference to DNA and RNA. A nucleic acid base attached to ribose forms a ribonucleoside. Adenine combined with ribose produces the nucleoside adenosine. When an oxygen atom is removed from the second carbon of ribose, the sugar unit formed is... 

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. 

A search for antimetabolites, i.e. analogues of essential metabolites that might displace the latter in vital processes, was proposed as a rational approach to the discovery of antibacterial agents, but it has had little success other than the achievements in the folic acid field (Section 1.06.6). Substances that resemble the components of nucleic acids have, however, had considerable success in the chemotherapy of cancer and of some virus diseases and in the suppression of the immune response. They may act by becoming incorporated in false nucleic acids or by blocking the synthesis of nucleic acids, nucleotides, nucleosides or of the pyrimidine and purine bases cytosine (88), thymine (89 R = Me), adenine (90) and guanine (91 X = CH). The simplest antimetabolites are analogues of these bases. 

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... 

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