Significance of the 3′ End in Nucleic Acid Chains: Implications in Molecular Biology and DNA Sequencing

3′ end

c, g

In molecular biology, the term 3′ end refers to the end of a nucleic acid chain (DNA or RNA) which has a free hydroxyl (-OH) group attached to the 3′ carbon of the sugar molecule that makes up the backbone of the chain. The 3’ end is opposite in direction to the 5’ end, which has a free phosphate (-PO4) group attached to the 5′ carbon of the sugar molecule.

In DNA sequencing and PCR amplification, the 3′ end is the site where DNA polymerase adds nucleotides to the chain of the growing DNA strand during synthesis, since nucleotides can only be added to the 3′ hydroxyl group. Thus, the 3′ end of a DNA strand is the one that is synthesized last and determines the direction in which a strand grows. In RNA molecules, the 3′ end often contains a poly(A) tail, a long tail made up of a stretch of adenosine nucleotides, which stabilizes the RNA molecule and affects its stability, translation, and processing.

More Answers: