Although many features can be shared with DNA, the RNA molecules possess several specific differences.

As apparent from its name, the sugar moiety in RNA, to which the phosphate and the nitrogen bases are attached, is ribose rather than the 2′deoxyribose of DNA. Ribose contains a 2′ hydroxyl group not present in deoxyribose.

RNA contains the pyrimidine uracil (U) in place of thymine, which is characteristic of DNA molecule. Uracil, like thymine, can form a base pair with adenine by two hydrogen bonds. However, it lacks the methyl group present in thymine. It may be noted that in one case, however, RNA possesses thymine.

The native RNA is single stranded rather than a double-stranded helical structure characteristic of DNA. However, given the double-stranded pattern, in the region of hairpin loops, A pairs U, and G pairs with C. Guanine can also form a base pair with uracil but is less stronger than G—C base pairs with C. Guanine can also form a base pair with uracil but is less stronger than G—C base pair. The base pairing in RNA hairpins is frequently imperfect. The apposing bases may not be complementary, and one or more bases of a single strand may be complementary and one or more bases along a single strand may be looped out to facilitate the pairing of others. The proportion of helical regions in various types of RNA varies over a wide range, and 50% is typical.

Since the RNA molecule is a single-stranded and complementary for only one of the two stands of a gene, it need not have complementary base ratios. In other words, its adenine content does not necessarily equal its uracil content, not does its guanine content necessarily equal its cytosine content.

RNA can be hydrolysed by weak alkali (pH 9) at 100°C) to 2′ 3′cyclic diesters of mononucleotides via as intermediate compound called 2′-3′-5′-triester. This intermediate, however, cannot be formed in alkali-treated DNA because of the absence of 2′ hydroxyl group in its molecule. Thus, RNA is alkali labile, whereas DNA is alkali stable.