Nucleic acid bases with formaldehyde

Formaldehyde administered by larval feeding therefore induces a wide variety of major genetic effects, which contrasts with the simple base pair changes largely found to be induced by nucleic acid base-analogues in prokaryotes. Several mutagenic purine and pyrimidine base-analogues of this latter type have been tested on Drosophila larvae, but found not to induce mutation [10] namely, 2-aminopurine 2,6-diaminopurine 5-bromodeoxyuridine and 5-bromodeoxycytidine. 

In general, the mechanism of heat and alkaline solution for DNA extraction may be based upon a hypothesis, previously proposed for the AR technique.32 Strong alkaline solution may denature and hydrolyze proteins, resulting in breaking cell and nuclear membranes as well as disrupting cross-linkages due to formalin fixation. It is no surprise to observe the similarity between retrieval of nucleic acid and retrieval of protein (antigen) based on a similar chemical reaction of formaldehyde with these two kinds of macromolecules (Fig. 3.1).15"19... 

Another obvious requirement of a nonaqueous solvent is chemical stability under a variety of conditions. Thus, methanol, especially after standing in the presence of air, may contain small amounts of formaldehyde which can react with groups on proteins and nucleic acids. Forma-mide, A, A-dimethylformamide, and related compounds, are slowly decomposed by acid or base in the solvent, and the possibility exists that such decomposition may be catalyzed to some extent by a protein dissolved in the solvent. Thus Rees and Singer (1956) found that the apparent osmotic pressure of a solution of insulin in lV,A -dimethylformamide continually increased over a period of a week at 25°C but reached equilibrium at 13.8°C, which might have been due to the slow decomposition of the solvent on the solution side of the osmotic membrane at the higher temperature. 

Nondiamine chemical reduction stains use silver nitrate to provide silver ions for reaction with protein and nucleic acid sites under acidic conditions (Merril, 1986, 1990). Image development is initiated by placing the gel in an alkaline solution, using sodium carbonate and/or hydroxide or other bases to maintain the alkaline pH, while the silver ions are selectively reduced to metallic silver with formaldehyde. The formic acid, produced by the oxidation of formaldehyde, is buffered by the sodium carbonate. This type of stain is relatively rapid and simple to perform. The nondiamine stains generally work best with gels 1 mm or less in thickness. 

Formaldehyde. Formaldehyde (like many other aldehydes or ketones) reacts with the amino groups of free bases or single-stranded nucleic acids. Since it can react with accessible amino groups, formaldehyde is used to measure the kinetics of nucleic acid unwinding (8). The chemistry is not well understood (possibly a Schiff s base as an intermediate). There is a detailed review by Feldman (9) on the subject. 

FIGURE 1.8 Some chemical reactions of bases and nucleotides, (a) Hydrolysis of a dinucleotide by alkali. Bases are denoted by B1 and B2. R denotes ribose or deoxyribose. (b to k) Chemical reactions (b) bisulfite, (c) chloroacetaldehyde, (d) diethyl pyrocarbonate, (e) dimethyl sulfate, (f) formaldehyde, (g) glyoxal, (h) hydrazine, (i) nitric acid, (j) nitrous acid, and (k) osmium tetroxide. Partly from R. L. P. Adams, J. P. Knowler, and D. P. Leader (1986). In The Biochemistry of the Nucleic Acids, 10th ed., pp. 5—34. Chapman Hall, with permission. 

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