Alkali lability

DNA is not susceptible to alkaline hydrolysis. On the other hand, RNA is alkali labile and is readily hydrolyzed by dilute sodium hydroxide. Cleavage is random in RNA, and the ultimate products are a mixture of nucleoside 2 - and 3 -monophosphates. These products provide a clue to the reaction mechanism (Figure 11.29). Abstraction of the 2 -OH hydrogen by hydroxyl anion leaves a 2 -0 that carries out a nucleophilic attack on the phosphorus atom of the phosphate moiety, resulting in cleavage of the 5 -phosphodiester bond and formation of a cyclic 2, 3 -phosphate. This cyclic 2, 3 -phosphodiester is unstable and decomposes randomly to either a 2 - or 3 -phosphate ester. DNA has no 2 -OH therefore DNA is alkali stable. 

RNA can be hydrolyzed by alkali to 2 3 cyclic diesters of the mononucleotides, compounds that cannot be formed from alkah-treated DNA because of the absence of a 2 -hydroxyl group. The alkali lability of RNA is useful both diagnostically and analytically. 

Kuhn and Low149 (see also, Ref. 150) were the first to recognize that glycosidic linkages that are) to a carbonyl group are alkali-labile, and are... 

Recently, Sage and Haseltine (49) have quantitatively determined the spectrum of DNA lesions induced by reactions of BPDE with DNA. They found that alkali-labile lesions account for about 40% of the DNA adducts. There was a striking correlation between the mutation frequencies induced by BPDE in lacl and the frequencies of alkali sensitive lesions at G, A, and C residues. Apurinic/apyrimidinic sites are common alkali-sensitive lesions. Earlier work by Drink-water e al. (48) had also shown that treatment of DNA with BPDE generated apurinic/apyrimidinic sites. 

The position was somewhat clarified by the isolation of 2- and 3-O-phos-phonucleosides from ribonucleic acid hydrolyzates in 92 to 100% yields,134 and also by the demonstration that 5-O-phosphonucleosides are also present in enzymic digests.49, 197 Yet this information gave no indication of the nature of the alkali-labile linkages. Thus, while the majority of the experimental evidence pointed to the phosphoryl residues as being doubly esterified with adjacent nucleosides, two facts remained apparently inexplicable on the basis of this type of structure. First, ready fission by alkalis, and secondly, the absence of 5-phosphates from alkaline hydrolyzates and their presence in enzymic digests. Both these facts have been explained by Brown and Todd in the following way.92... 

Of wider significance was the generation of 2-phenylethyl radical by oxyhemoglobin-mediated oxidation of phenelzine (2-phenylethylhydrazine), which was shown to be more efficient in promoting alkali-labile sites than in producing direct DNA strand scission (Fig. 6) [25]. 

Such studies, and others on an O-phosphonomannan155 and a tei-choic acid,168 relied on judicious comparisons (of shift) with signals of model compounds, and these are simpler than conventional, analytical procedures. For example, it is difficult to methylate alkali-labile O-phosphonomannans, and sialic acid and KDO-containing polymers would require difficultly available, O-methylated standards. In addition, periodate-oxidation analyses are restricted to polymers having fortuitously amenable, chemical structures. 

Hartley4 has shown that chemical oxidation of O.M.P.A. using potassium permanganate leads to the transfer of one oxygen atom per molecule of O.M.P.A. An alkali-labile substance of increased anticholinesterase activity was thereby produced. 

Compound (V) (see p. 88) is a less active inhibitor in vitro than its toxicity1 might suggest. As has already been pointed out it is a quick-acting poison. Oxidation by permanganate in this case is very slow, but here also an alkali-labile material of increased inhibiting power is produced, but in small yield. 

Seto B. 1980. Chemical characterization of an alkali-labile bond in the polypeptide of proline reductase from Clostridium sticklandii. J Biol Chem 255 5004-6. 

Single and double strand breaks and alkali labile sites... 

Figure 4.1 The comet assay. A single-cell suspension is embedded in agarose on a slide. Cells are then subject to lysis followed by electrophoresis. If present, damaged DNA migrates out of the nucleoid structure during electrophoresis to producing a characteristic comet shape. Double-strand breaks are revealed under neutral conditions, whereas alkali conditions additionally show single-strand breaks and alkali labile sites. Image analysis of stained DNA is used to quantitate the amount of damaged DNA in the comet tail.

This system allows the separation of alkali-labile proteins (e.g., acylphosphate phosphoproteins) under denaturating conditions according to their molar mass. Despite the low acrylamide concentration (%T = 5.61, %C = 3.61), the separation force is remarkable. Because it is a SDS-containing system, the migration is from to + despite the low pH. 

A lot of biologic membrane systems and cellular organelles contain kinases, which transfer phosphate groups to proteins, especially to serine, threonine, and tyrosine residues. Self-phosphorylation of enzymes leading to acylphosphates or phosphoamides can be observed, too. With respect to their chemical stability, these phos-phoproteins are classified into acid-stable (alkali labile), hydroxyl-amine-sensitive, and acid labile. 

Photolysis of a frozen aqueous solution of thymine at 254 nm gives a major product with a reported quantum yield of 1-2,31 and a minor product.32 The abundance ratio of the two products is about 8. The major product is the known thymine dimer.7,10 Identity of the minor product is unknown photolysis of it in solution produces thymine and a dimeric product which chromatographs like the major product. This minor product is alkali labile. Existence of other products in the thawed photolysis solution is suggested by details of the spectrum.32... 

Figure 10 shows that the values of kag for the oxidation of G and GG are close to one another, and are smaller by a factor of only -1.7 than the value of kag for the oxidation of guanine in the GGG sequence. Estimates by Lewis et al. [89] have shown that even small differences in the rate constants can provide modest selectivities for alkali-labile strand cleavage observed in a number of experimental studies [83-90]. 

DIA, DNA strand breaks/alkali-labile sites, Syrian hamster embryo cells + NT 200 Parent Casto (1979)... 

DIH, DNA strand breaks, alkali labile site, human bronchial epithelial + NT 200 Chang et al. (1990)... 

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