Base Deamination

Base deamination is accelerated by nitrous acid and sodium bisulfite. Nitrous acid nonspecifically promotes base deamination in both double-stranded and single-stranded DNA. In contrast, sodium bisulfite specifically promotes cytosine deamination in single-stranded DNA. Some single-stranded regions do exist in cellular DNA, at least temporarily—for example, during transcription. In some cases, sodium bisulfite is used as a food additive. It is also used in the wine industry. 

In mammalian genomes, some cytosine residues of the CpG (cytosines adjacent to guanines) sequences in DNA are methylated, forming 5-methylcytosine. Deamination of 5-methylcytosine, however, yields thymine, a normal base component of DNA. In single-stranded DNA, this is a challenging problem as cells are not able to determine that this thymine is abnormal. In double-stranded DNA, however, deamination of the 5-methylcytosine in a methylated C G base pair yields a T G mismatch. Cells are therefore able to distinguish the thymine in a T G mismatch as 

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DNA base deamination studies employing A-nitroso-2-hydroxymorpholine and calf thymus DNA indicate that A-nitroso-2-hydroxymorpholine may deaminate the primary amino groups in DNA via nitroso transfer reactions in vivo (Loeppky et al., 1994). 

Glaser R, Rayat S, Lewis M, et al. (1999). Theoretical studies of DNA base deamination. 2. Ab initio study of DNA base diazonium ions and of their linear, unimolecular dediazoniation paths./. Am. Chem. Soc. 121 6108-6119. 

This is small nucleolar RNA or snoRNA. These RNA species recognize their target sequence by base-pairing and then recruit specialized proteins that perform nucleotide modifications to these RNAs usually 2 O-ribose methylation, base deaminations such as adenine-to-inosine conversions, and the addition of pseudouridines. These modifications are crucial to ribosome biogenesis. 

Oldreive C, Zhao K, Paganga G, Halhwell B, Rice-Evans C. Inhibition of nitrous acid-dependent tyrosine nitration and DNA base deamination by flavonoids and other phenohc compounds. Chem Res Toxicol 1998 11 1574-1579. 

Thus, in contrast to benzothiepins, dibenzo compounds can be synthesized by direct acid-catalyzed elimination of water from hydroxy derivatives, or of amines from amino derivatives, at elevated temperatures due to their thermal stability. As in the case of benzothiepins, dibenzo derivatives can also be prepared by base-catalyzed elimination from the corresponding halo derivatives however, the yields are somewhat lower compared to the acid-catalyzed reactions. As a special case, an aziridine derivative was deaminated by palladium-catalyzed hydrogenation to afford the corresponding dibenzothiepin.69... 

Note Such enamines usually react as alkenes but with deamination the dienamines also react as alkenes but usually without deamination. No added base is needed for these reactions. 

Protoadamantanone has been prepared by the nitrous acid deamination of 2-amino-l-adamantanol (77%), by aprotic diazo-tization of endo-7-aminomethylbicyclo[3.3.1]nonan-3-one in benzene with an equivalent amount of acetic acid (67%), and by thermolysis of 1-adamantyl hypohalites followed by base-promoted cyclization of the resulting halo ketones (32-37%)." In spite of low and erratic yields, the last reaction sequence has provided the most convenient route to the protoadamantanes, since the other two approaches require lengthy syntheses of the starting materials. 

The susceptibilities of some of these fluorinated purine nucleosides to the action of enzymes are now described. In contrast to the inertness of the 2 -deoxy-2 -fluoro- and 3 -deoxy-3 -fluorocytidine analogs 739, 744, and 821 towards cytidine deaminase, the adenosine compounds 867, 883, and 906 are readily deaminated - by the adenosine deaminase in erythrocytes and calf intestine, but the resulting (deaminated) inosine compounds (from 867 and 883), as well as 888, are highly resistant - to cleavage by purine nucleoside phosphorylase (to give hypoxanthine base for the first two). The reason was discussed. Both 867 and 883 can form the 5 -triphosphates, without deamination, in human erythrocytes or murine sarcoma cells in the presence of 2 -deoxycoformycin, an adenosine deaminase inhibitor, but... 

Figure 36-23. Base excision-repair of DNA. The enzyme uracil DNA glycosylase removes the uracil created by spontaneous deamination of cytosine in the DNA. An endonuclease cuts the backbone near the defect then, after an endonuclease removes a few bases, the defect is filled in by the action of a repair polymerase and the strand is rejoined by a ligase. (Courtesy of B Alberts.)...

N-Nitrosamides are much less stable than the parent N-nitros-amines and they can decompose by either thermal, photolytic or acid and base (nucleophilic) catalysed pathways Thermal decomposition has attracted much attention as a clean method of deamin-... 

We have also shown ( 8) that other bases stronger than CH-CX) (pK. 4.75) catalyse the decomposition of N -nitroso-2-pyrrolidone at o C. With the exception of imidazole, these reactions follow uncomplicated second order kinetics (Rate = kp[Substrate][Base]) and only products of deamination (hydrolysisT are obtained. Generally, values increase with the base strength of the catalyst and fit tne Br/e(nsted relationship withes 0.66. However, the absence of significant catalysis by sterically hindered bases 2,6-lutidine), the strong catalysis by imidazole relative to HPOi (k2(Imidazole)/k2(HP0J ) = 83) and by hydroxide ion relative to... 

The deamination of primary amines such as phenylethylamine by Escherichia coli (Cooper et al. 1992) and Klebsiella oxytoca (Flacisalihoglu et al. 1997) is carried out by an oxidase. This contains copper and topaquinone (TPQ), which is produced from tyrosine by dioxygenation. TPQ is reduced to an aminoquinol that in the form of a Cu(l) radical reacts with O2 to form H2O2, Cu(ll), and the imine. The mechanism has been elucidated (Wihnot et al. 1999), and involves formation of a Schiff base followed by hydrolysis in reactions that are formally analogous to those involved in pyridoxal-mediated transamination. 

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. ... 

The analogons deamination reaction is not observed in l-methyl-2 -deoxy-adenosine nncleosides. ° Rather, in the adenine series, the Dimroth rearrangement occnrs (Scheme 8.4). On the contrary, in styrene adducts of 2 -deoxyadenosine, the hydroxyl residue of the adduct undergoes intramolecular reaction with the base to initiate deamination (Scheme 8.6). ° ° Similarly, cytosine residues bearing styrene adducts at the N3-position undergo rapid deamination (nearly complete deamination is seen within 75h). °°... 

Process development of the synthesis of iodoaniline 28 began with an improved synthesis of l-(4 -aminobenzyl)-l,2,4-triazole (6) (Scheme 4.7), which was prepared in the medicinal chemistry synthesis, albeit with poor regioselectivity (Scheme 4.1). We found that this aniline intermediate 6 could be readily prepared in three steps in >90% overall yield from 4-amino-l,2,4-triazole (30) and 4-nitrobenzyl bromide (4) based on a modified literature procedure [9]. The condensation of 30 and 4 in isopropyl alcohol followed by deamination gave the nitro... 

More-specific methods are available for identifying and quantitating the typical, amino sugar component of heparin (and some heparan sulfate species), namely, 2-deoxy-2-sulfoamino-D-glucose. Most of these methods are based on conversion of these residues into 2,5-anhydro-D-mannose by deamination with nitrous acid (see Section VIII,2). The 2,5-anhydro-D-mannose residues may be determined either colorimetrically,52-54 or fluorimetrically.55... 

The DNA bases that contain amino groups tend to deaminate spontaneously. In particular, cytosine significantly deaminates to uracil, but adenine and guanine can also deaminate to hypoxanthine and xanthine, respectively. If not corrected, the new bases can cause serious mutations... 

Not all mutagenesis in IS. coli is dependent on SOS-processing. Mutations may arise quite simply during DNA replication if a base is substituted by or converted to another, incorrect, base. Consider the consequence of oxidative deamination of the base 5-methylcytosine to thymine. Replication followed by daughter strand segregation will result in a G C base pair having been mutated to an A T base pair. Sites containing 5-methylcytosine are hotspots for G C to A T transitions in 12. coli (24). 

Figure 27.2 Treatment of cytosine bases with bisulfite results in a multi-step deamination reaction, ultimately leading to uracil formation.

Since the site of modification on cytosine bases is at a hydrogen bonding position in double helix formation, the degree of bisulfite derivatization should be carefully controlled. Reaction conditions such as pH, diamine concentration, and incubation time and temperature affect the yield and type of products formed during the transamination process. At low concentrations of diamine, deamination and uracil formation dramatically exceed transamination. At high concentrations of diamine (3M), transamination can approach 100 percent yield (Draper and Gold, 1980). Ideally, only about 30-40 bases should be modified per 1,000 bases to assure hybridization ability after derivatization. 

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