Directionality and purine–pyrimidine pairing

Molecules (Unity and diversity) · Nucleic acids · note 5 of 7

Spec A1.2.11, A1.2.12

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Directionality and purine–pyrimidine pairingSpec A1.2.11, A1.2.12

In short

Nucleic acid strands have directionality because each phosphate links carbon 3' of one sugar to carbon 5' of the next, giving a 5' end and a 3' end. New strands are built only 5' to 3', and ribosomes read mRNA 5' to 3'. Each base pair is a purine with a pyrimidine, so the helix is uniform.

Directionality of RNA and DNA

The carbons of the pentose sugar are numbered 1' to 5'. The base is attached to carbon 1', the phosphate of the same nucleotide to carbon 5', and the phosphate of the next nucleotide to carbon 3'. So every link in the backbone runs from carbon 3' of one sugar to carbon 5' of the next. One end of a strand has a free phosphate on carbon 5' (the 5' end) and the other a free OH on carbon 3' (the 3' end). In DNA the two strands run in opposite directions: this is what antiparallel means.

Why directionality matters
Process	Significance of 5' to 3'
Replication	DNA polymerase can only add nucleotides to the 3' end of a growing strand, so new DNA is built 5' to 3'
Transcription	RNA polymerase builds mRNA 5' to 3', so it moves along the template strand reading it 3' to 5'
Translation	Ribosomes read mRNA from the 5' end towards the 3' end, codon by codon

Purine-to-pyrimidine bonding

Adenine and guanine are purines, with two rings. Cytosine, thymine and uracil are pyrimidines, with one ring. Each base pair in DNA is one purine bonded to one pyrimidine (A–T and C–G), so all base pairs have equal length. The two backbones are therefore always the same distance apart and the DNA helix has the same three-dimensional structure, regardless of the base sequence. This uniformity contributes to the stability of the helix.

A DNA ladder of three base pairs with carbons 1′, 3′ and 5′ labelled on one nucleotide, 5′ ends with a free phosphate and 3′ ends with a free OH, arrows showing each strand running 5′ to 3′ in opposite directions, and purines drawn as two rings and pyrimidines as one ring so every base pair has equal width. — Each strand runs 5′ to 3′, in opposite directions. Every base pair is a purine (two rings) with a pyrimidine (one ring), so all base pairs have equal width.

Common mistake:

A purine never pairs with a purine. Two purines would be too wide to fit between the backbones and two pyrimidines too narrow.

Written and checked against the IB Biology HL specification · Updated October 2026

Frequently asked questions

What is the structure of a DNA nucleotide?

A DNA nucleotide has a phosphate group, the pentose sugar deoxyribose and a nitrogenous base, which is adenine, thymine, guanine or cytosine. The phosphate and base are attached to the sugar on opposite sides. Nucleotides link through sugar–phosphate bonding to form a strong covalent backbone with the bases sticking out.

Why is DNA described as antiparallel?

DNA is described as antiparallel because its two strands run in opposite directions. The strands are held together by hydrogen bonds between complementary bases, adenine with thymine and guanine with cytosine. In diagrams, one strand is drawn upside down relative to the other to show this.

What are the main differences between DNA and RNA?

DNA is double-stranded, while RNA is single-stranded. DNA contains the base thymine, while RNA has uracil instead. DNA contains the sugar deoxyribose, while RNA contains ribose, which has an OH group on carbon 2 where deoxyribose has only hydrogen. Examples of RNA are mRNA, tRNA and rRNA.

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