The mechanism of C-binding: depurination and beta-elimination

Abstract

C-banding of chromosomes involves the differential solubilization of fragmented DNA from euchromatin by three sequential treatments: 1. Acid, 2. Mild base, 3. Hot salt. The data indicate solubilization is effected by 1) depurination, 2) DNA denaturation, 3) chain breakage of the depurinated sites respectively in the three treatments. Conditions were found wherein each treatment in proper sequence was necessary for C-banding and the appropriate chemical reactions were measured in these treatment conditions. The acid treatment (0.2 N HCl) depurinates chromosomal DNA at the rate of 0.26 x 10(-6) purines/dalton min to an alkaline molecular weight of 10(5) daltons but does not break the depurinated sites. Bleomycin can substitute for acid as a base removing agent. Sodium borohydride, by reducing the depurinated sugar's aldehyde thereby preventing chain breakage by the beta-elimination reaction, reversibly inhibits DNA-extraction. Chain breakage at the DNA's apurinic sites occurs not in the 2 min mild alkali treatment where the half-life for breakage is 26 min but in the 18 h hot salt treatment where the half-life for chain breakage is 1-2 h. Most of the DNA extraction occurs in the hot salt as 10(5) dalton fragments as measured in formamide gradients. Bleomycin is introduced as a substitute for HCl; it removes nitrogenous bases from DNA in situ while better preserving the morphology of the final C-banded chromosomes.