Adenine, alkylation

An interesting alkylation reaction for purines, such as adenine or xanthine, by tetrabutylammo-nium fluoride catalyzed alkylation with trialkyl phosphates has been recently described. This reaction also works for the corresponding nucleosides and nucleotides with high yield. In the case of adenine, alkylation gives predominantly the N9 product 22. ... 

Papirmeister B, Dorsey JK, Davison CL et al. (1970). Sensitization of DNA to endonuclease by adenine alkylation and its biological significance. Fed Proc, 29, 726. 

Fig. 2 Methyltransferase-directed N -adenine alkylation of DNA by 5 -[(5)-[(3S)-3-amino-3-carboxylpropyl]( )-pent-2-en-4-ynylsulfonio]-5 -deoxy-adenosine and subsequent CuAAC reaction with an azido-modified reporter group [83]...

Adenine, N -ethyl-N -hydroxyethyl-intramolecular alkylation, 5, 531 Adenine, N -formylmethyl-... 

Amine bases in nucleic acids can react with alkylating agents in typical Sjsj2 reactions. Look at the following electrostatic potential maps, and tell which is the better nucleophile, guanine or adenine. The reactive positions in each are indicated. 

DNA sequencing and. 1113 Electrospray ionization (ESI) mass spectrometry, 417-418 Electrostatic potential map, 37 acetaldehyde, 688 acetamide, 791,922 acetate ion. 43. 53, 56, 757 acetic acid. 53. 55 acetic acid dimer, 755 acetic anhydride, 791 acetone, 55, 56. 78 acetone anion, 56 acetyl azide, 830 acetyl chloride, 791 acetylene. 262 acetylide anion, 271 acid anhydride, 791 acid chloride, 791 acyl cation, 558 adenine, 1104 alanine, 1017 alanine zwitterion, 1017 alcohol. 75 alkene, 74, 147 alkyl halide, 75 alkyne. 74... 

A crosslinking mechanism based on these data was proposed. Initial monoalkylation at guanine is followed by a template-directed alkylation at either guanine or adenine two base pairs away on the opposite strand. In support of this, Armstrong... 

Saito et al. achieved the first direct confirmation of double alkylation of purine bases by azinomycin B [140]. They incubated azinomycin B with the self-comple-mentary DNA duplex d(TAGCTA)2 and monitored the reaction by HPLC and ion spray MS. They observed initial formation of a monoadduct that was then converted into a crosslinked bisadduct. The crosslink position was identified as between the guanine of one strand and the 5 -adenine on the other strand by thermo-lytic depurination. Further decomposition prevented structural analysis of the azi-... 

It was concluded that the crosslinking reaction proceeded through initial alkylation of N-7 of adenine by the aziridine ring, followed by guanine N-7 alkylation by the epoxide (Figure 11.12). This seems inconsistent with Armstrong s earlier conclusions, but the very short oligonucleotides used by Saito et al. may influence the DNA alkylation chemistry. 

Lindblom and Blander (1980) have given a number of examples of relevance in the pharmaceutical industry. These include C-alkylations, 0-alkylations, and A-alkylations. The C-alkylation of phenylacetonitrile, (mono- and di-) alkylation of benzylpenicillin with a-chlorodiethyl carbonate (where the acid part and the halide part in the esterification would have degraded quickly under normal conditions adopted for the reaction), A-alkylation of purines and adenine, etc. are discussed at some length and the supremacy of PTC is clearly shown. 

Alkylation of Adenine and Cytosine Residues can Accelerate Deamination 341... 

Deamination, the hydrolytic loss of exocyclic amino groups on the DNA bases, is typically a very slow reaction. For example, deamination of cytosine residues in dnplex DNA occnrs with a half-life of about 30,000 years under physiological conditions, and the deamination of adenine residues is still more sluggish. " Alkylation at the N3-position of cytosine (Scheme 8.5) greatly increases the rate of deamination (ty2 = 406 h). Deamination of 3-methyl-2 -deoxycytidine proceeds 4000 times faster than the same reaction in the unalkylated nucleoside. Alkylation of the N3-position in cytosine residues also facilitates deglycosylation (Jy2 = 7700 h, lower pathway in Scheme 8.5), but the deamination reaction is 20 times faster and, therefore, predominates. ... 

Base-pairing interactions have been realized in metal complexes by extending ligand functionalization to include two complementary nucleobases (136). Sequential alkylation of 1,2-dithioethane using 2-chloroethyl-9-adenine and 3-chloropropyl-l-thymine yields the AT-... 

The reversibility of QM adducts also creates numerous challenges. For example, measuring the full burden of DNA alkylation by a QM can be obscured by the loss of its labile products during or before chemical identification can be completed. Results from a deoxynucleotide model system indicated that only a small fraction of the possible adducts could be measured after the interval required for analysis of DNA. Perhaps the kinetic products of QMs also contribute to the cellular activity of these intermediates although this has yet to be explored. QM equivalents can be envisioned to migrate from one reversible nucleophile such as the N1 of adenine in such cofactors as ATP to another until quenched by a compound such as glutathione that is present in cells as a defense against undesirable electrophiles. 

The primary binding site of adenine is N(9) but when this is blocked as in adenosine it becomes N(l). This makes the binding of metals to adenosine weaker than the binding to N(7) of guanosine. The N(7) of guanosine is a known major site of alkylation too. 

The mechanism of action of alkylating agents is complex. Adenine and guanine are easily alkylated. Guanine is alkylated primarly at position 7 and adenine at position 3. The reaction produces an exceedingly labile glycosidic bond. Splitting of this bond leads to depurination. 

In the early days of meteorite analysis, it was difficult to detect N-heterocycles later, the Murchison meteorite was shown to contain xanthine, hypoxanthine, guanine, adenine and uracil (about 1.3 ppm in total). This meteorite seems to contain various classes of basic and neutral N-heterocycles, as well as isomeric alkyl derivatives. 

Solomon JJ, Segal A. 1985. Direct alkylation of calf thymus DNA by acrylonitrile. Isolation of cyanoethyl adducts of guanine and thymine and carboxyethyl adducts of adenine and cytosine. Environ Health Perspect 62 227- 230. 

It can be seen that alkylation has changed the sugar-base conformation (distant from the site of alkylation) from anti (as in deoxyadenosine and in B-DNA) to syn (as in alkylated deoxyadenosine and in some bases in Z-DNA). The sugar puckers are either C2 -endo or C3 -endo. A second structural feature of great interest in these crystals is that the more planar anthracene portion of the PAH is stacked between adenine residues of other molecules throughout the crystal. The highly buckled region of the PAH does not take part... 

Figure 26. Stacking of PAHs and bases in alkylated adenosine and deoxyadenosine derivatives, (a) The methylanthracenyl derivative of adenosine, (b) The DMBA derivative of deoxyadenosine viewed onto the planes of adenine groups, (c) Side view of this.

Methods currently available for chemiluminescent detection of nucleic acids are not based on derivatization techniques that directly recognize one of the nucleic acid bases or nucleotides. For chemical derivatization-based chemiluminescent detection, the specific reactivity of alkyl glyoxals and arylglyoxals with adenine or guanine nucleotides has been investigated. 

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