Nucleic acid bases reactions

Kinoshita, Imoto etal.11 14) synthesized other anionic models, 5 (APVP), CPVP, UPVP, TPVA, HPVA, THPVA, and 6 (AMPPVA), by the polymer reaction of N-eoupled(2-dihydrogenphosphate)-ethylderivatives of nucleic acid bases (or adenosine-5 -phosphate, AMP) with polyvinylaleohol. A, C, U, T, H, and TH denote adenine, cytosine, uracil, thymin, hypoxanthine, and theophylline, respectively. The authors reported the apparent hypochromities of 3 to 16% for many kinds of mixtures of the models and DNA or RNA, as compiled in Table 1. However, for the mixtures APVA + RNA, HPVA + RNA HPVA + DNA, THPVA + RNA, CPVA + DNA and CPVA + RNA, no hypochromicity was detected. 

Upon absorption of UV radiation from sunlight the bases can proceed through photochemical reactions that can lead to photodamage in the nucleic acids. Photochemical reactions do occur in the bases, with thymidine dimerization being a primary result, but at low rates. The bases are quite stable to photochemical damage, having efficient ways to dissipate the harmful electronic energy, as indicated by their ultrashort excited state lifetimes. It had been known for years that the excited states were short lived, and that fluorescence quantum yields are very low for all bases [4, 81, 82], Femtosecond laser spectroscopy has, in recent years, enabled a much... 

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. 

Two principal types of nucleic acid-based methods, nucleic acid hybridization and polymerase chain reaction (PCR), are commonly used for the rapid identification of bacteria. A few other nucleic acid-based methods will also be mentioned. 

There is always interest in the photochemistry of the pyrimidine nucleic acid bases and related simple pyrimidinones, due to its importance in genetic mutation. In addition to damaging DNA, photo-induced reactions may also repair the damage, as in the reduction, by FADH, of the thymine glycol 64 back to thymine <06JACS10934>. Another report related to repair of DNA involved a model study, by means of the linked dimer 65, of the involvement of tryptophan in the electron-transfer leading to reversion of thymine oxetane adducts <06OBC291>. 

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 photolytic activation of 5m was also shown to lead to DNA cleavage [33,35-38]. This reaction appeared to be faster and more efficient than the Cu+-catalyzed cleavage conditions. The mechanism(s) of DNA cleavage should be different because aryl cations (not aryl radicals) are believed to be produced under photolytic conditions (Fig. 12) [7]. Such electrophiles should target the nucleic acid bases and/or the positively charged phosphodiester backbone, and both of these could lead to DNA cleavage. 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

Photocycloaddition and photoaddition provide good models for the mechanism by which ultraviolet light can cause damage to nucleic acids. When ultraviolet light damages DNA, the principal reactions occurring involve the nucleic acid bases. Photocycloaddition reactions to form... 

Incorporation of nucleic acid bases by polymer modification reactions... 

The reaction of the p-nitrophenyl esters with the polymer (4) was studied in dimethyl sulfoxide ( DMSO ) solution in the presence of triethylamine at 25°C. The poly-L-lysine derivatives obtained have different IR absorption spectra from those of the starting compounds, and have absorptions assigned to the nucleic acid bases. Poly( e,N-Ade-L-lysine )(5) was soluble in DMSO and ethylene glycol, and also in water below pH 3, where it was present as a protonated form. In dimethylformamide (... 

In relation to these works, the reaction of p-nitrophenyl esters with optically active poly( propyleneimine )(8) was studied at 25°C in DMSO solution according to the same procedure described for the case of poly-L-lysine derivatives. The poly( propyleneimine ) derivatives thus obtained have different IR and UV absorption spectra from those of the starting compounds, and show absorptions assigned to the nucleic acid bases. However, their contents determined by UV spectroscopy were substantially low as compared with the case of poly-L-lysine derivatives for (9) and (20), the base contents were below 30 and 50 %, respectively. The result was explained by a steric hindrance caused by methyl groups on the main chain of poly( propyleneimine ) ... 

The latter, ester-type derivatives (21) were prepared by the reaction of L-glutamic acid with hydroxyethyl derivatives of nucleic acid bases. The reaction was studied in the presence of p-toluenesulfonic acid at 100-110°C in dioxane, and water formed was removed by azeotropic distillation with dioxane ( ). 

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. 

Nucleic acid-based technologies Nucleic acid probe Polymerase chain reaction, DNA amplication 16S rRNA sequencing techniques automated riboprinting... 

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]. 

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]. 

Guanine is the most easily oxidizable natural nucleic acid base [8] and many oxidants can selectively oxidize guanine in DNA [95]. Here, we focus on the site-selective oxidation of guanine by the carbonate radical anion, COs , one of the important emerging free radicals in biological systems [96]. The mechanism of COs generation in vivo can involve one-electron oxidation of HCOs at the active site of copper-zinc superoxide dismutase [97, 98], and homolysis of the nitrosoperoxycarbonate anion (0N00C02 ) formed by the reaction of peroxynitrite with carbon dioxide [99-102]. 

The Michael addition of nucleic acid bases to dimethyl itaconate (137) has been utilized to prepare a number of condensation monomers (Scheme 39) (80MI11110). Reaction of active esters (138) with various diamines produces polyamides having the bases as pendant groups. 

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