The N-glycosidic bond, especially that formed by purine bases, is one of the most reactive covalent bonds in nucleic acids.

Just as in monomer units, N-glycosidic bonds in ribonucleosides of nucleic acids are more stable than in deoxyribonucleosides; within each class of nucleic acids, purine N-glycosidic bonds are more easily cleaved than pyrimidine ones. At present, cleavage of N-glycosidic bonds is broadly employed in analysis of the primary structure of nucleic acids. There are two methods for cleaving these bonds in the latter: direct, when the N-glycosidic bonds is hydrolysed by the action of an acid, and indirect, when hydrolysis is preceded by modification of particular bases so that the linkage between them and the carbohydrate moiety is significantly labilized.

9.3.1 Direct Hydrolysis Methods

The hydrolysis of N-glycosidic bonds in polymeric molecules is accompanied by cleavage of internucleotide linkages. These processes may be independent in RNAs, whereas in DNAs hydrolysis of N-glycosidic bonds is followed by depolymerization. Most likely, the mechanism of such hydrolysis in RNAs and DNAs is similar to that described in the context of nucleotides. In determining the nucleotide composition of DNA, N-glycosidic bonds are hydrolysed by 72% chloric acid (110⁰ C, 1 h) or 98-100% formic acid (175⁰ C, 2 h); in this case, all N-glycosidic bonds get cleaved. The use of dilute acids to depolymerize DNA results in polypyrimidine blocks and purine bases. For instance, partial depurination of DNA is observed when aqueous solutions are heated at pH 6-7.5 (65-100⁰ C) and complete depurination occurs at pH 2 (37⁰ C, 24 h, dilute hydrochloric acid). N-Glycosidic bonds in RNA are more difficult to break (just as in monomer units). When RNA is treated with 1 N hydrochloric acid (100⁰ C, 1 h), pyrimidine nucleoside 3'(2')-phosphates and purine bases are formed. Such acid hydrolysis is used to determine the nucleotide composition of RNAs.

9.3.2 Indirect Hydrolysis Methods

Since the alkylation of purines at N3 and N1 leads to a marked labilization of the N-glycosidic bond, nucleic acids can be alkylated to be depurinated. The hydrolysis of N-glycosidic bonds in DNA at methylated units occurs already at pH 7. When a methylated DNA is maintained at 37⁰ C (pH 7.2), the half-period of glycosidic bond hydrolysis is 25 h for 3-methyladenine and 140 h for 7-methylguanine. The hydrolysis rate is to some extent dependent on the species of the introduced alkyl group. For instance, adenines with an HOCH₂CH₂SCH₂CH₂ group at N3 are detached from the alkylated DNA with a half-life of 8 h under the same conditions.

These findings suggest that the N-glycosidic bond is labilized to a much greater degree after N3-alkylation of adenine, as compared to N7-alkylation of guanine. Comparison of the ease with which N7-alkylated adenines and guanines detach themselves from the nucleic acid indicates that the N-glycosidic bond formed by the former is more reactive in this case as well. Interestingly, the N1-alkylation of adenine virtually does not affect the strength of the glycosidic bond it forms. However, because of the much faster rate of DNA alkylation at N1 in guanines, the subsequent hydrolysis of N-glycosidic bonds in DNA proceeds primarily at guanines.

Worthy of mention among other reactions in which glycosidic bonds are hydrolysed is the one with preliminary opening of the heterocyclic rings. A rather common procedure is treatment of RNAs and DNAs with hydrazine or hydroxylamine to open pyrimidine rings. For example, the hydroxylamine linked to the ribose phosphate chain in uracil-free RNAs resulting from hydroxylamine treatment can be eliminated by hydrolysis in a weakly acidic (pH 5) medium in the presence of cyclohexanone. Uridines of the starting RNA are replaced in the resulting polymer by ribosyls with free glycosidic centers.

DNA does not contain bases reactive enough with respect to hydroxylamine at pH 10; however, the reaction can be conducted after deamination of DNA in the presence of nitrous acid, with cytosines being converted into uracils. In this way DNA can be cleaved specifically at cytosines.