- The 3′ hydroxyl group (-OH) is a critical chemical feature of the deoxyribose sugar in DNA and the ribose sugar in RNA, located on the third carbon atom of the pentose ring. Its importance lies in its role in forming the phosphodiester bond that links one nucleotide to the next during nucleic acid synthesis.
- DNA and RNA polymerases catalyze the addition of nucleotides by connecting the 5′ phosphate group of an incoming nucleotide to the 3′ hydroxyl group of the growing strand. This directional chemistry means that nucleic acids are always synthesized in the 5′ to 3′ direction, making the 3′ hydroxyl group indispensable for elongation.
- The absence of the 3′ hydroxyl group has profound biochemical consequences. In dideoxynucleotides (ddNTPs), for example, the sugar lacks both the 2′ and 3′ hydroxyl groups. When incorporated into a growing DNA strand, a ddNTP prevents further elongation because there is no 3′ hydroxyl available to form the next phosphodiester bond. This property is exploited in Sanger sequencing, where controlled incorporation of ddNTPs halts DNA synthesis at specific points, generating fragments that can be analyzed to determine DNA sequences. Similarly, some antiviral drugs, such as AZT (azidothymidine) used against HIV, mimic nucleosides but lack a functional 3′ hydroxyl group, thereby terminating viral DNA synthesis.
- In the context of cellular biology, the 3′ hydroxyl group also plays a role in repair, recombination, and transcription. DNA polymerases involved in replication and repair always require a free 3′-OH to initiate synthesis, which is why primers (short RNA or DNA sequences with a 3′-OH) are necessary for replication to begin. In RNA synthesis, RNA polymerases similarly extend transcripts by linking incoming nucleotides to the 3′-OH of the growing RNA chain. Furthermore, DNA damage that disrupts the 3′-OH terminus, such as strand breaks, can stall replication and transcription, often triggering DNA repair pathways to restore functional ends.
- From an evolutionary and structural perspective, the presence of the 3′ hydroxyl group distinguishes ribose in RNA (which has both 2′ and 3′ hydroxyl groups) from deoxyribose in DNA (which lacks the 2′ hydroxyl group but retains the 3′-OH). This subtle difference contributes to RNA’s chemical reactivity and versatility, while DNA’s relative stability makes it a better long-term repository of genetic information.
