The 5′ to 3′ direction describes the orientation of a DNA strand based on the numbered carbon atoms in each nucleotide’s deoxyribose sugar. A strand runs from its free 5′ phosphate end toward its free 3′ hydroxyl end.
This is additional higher level (AHL) content in IB Biology subtopic A1.2, Nucleic acids.
Why DNA Has Direction
The carbon atoms in deoxyribose are numbered 1′ to 5′. The 1′ carbon bonds to a nitrogenous base, while the 5′ carbon bonds to a phosphate group.
During formation of the sugartophosphate backbone, a phosphodiester bond forms between the phosphate attached to the 5′ carbon of one nucleotide and the hydroxyl group on the 3′ carbon of the previous nucleotide. Consequently, each strand has two chemically different ends.
| End | Defining feature |
|---|---|
| 5′ end | Free phosphate group attached to the sugar’s 5′ carbon |
| 3′ end | Free hydroxyl group attached to the sugar’s 3′ carbon |
The two strands in DNA are antiparallel: one runs 5′ to 3′, while the complementary strand runs 3′ to 5′.
Directionality is essential during DNA replication. DNA polymerase adds the 5′ phosphate of an incoming nucleotide to the free 3′ hydroxyl end of the growing strand. DNA can therefore be synthesized only in the 5′ to 3′ direction, while the template strand is read in the 3′ to 5′ direction. This produces continuous synthesis on the leading strand and discontinuous synthesis through Okazaki fragments on the lagging strand.
The same principle applies during transcription: RNA polymerase reads the DNA template 3′ to 5′ and synthesizes RNA 5′ to 3′.
A common misconception is that 5′ and 3′ indicate positions along the entire DNA molecule. They actually refer to carbon numbers within each nucleotide’s sugar.
Exam Technique
For an explain question, link sugar carbon numbering to antiparallel strands and then to polymerase action. Always state that new nucleotides are added to the 3′ end, so synthesis proceeds 5′ to 3′.
