Nucleic acid bases reactions with formaldehyde

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... 

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. 

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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