Biology · DNA, Replication & Repair

DNA structure, complementarity and chromosome organisation

Two rows of letters can look like duplicate messages. In DNA they are complementary sequences carried by oppositely oriented chemical chains. Knowing both the letters and the strand ends lets us predict a partner sequence and understand how copying will proceed.

Use the earlier ideas of nucleotides, complementary molecules, enzymes, inheritance and mutation. A nucleotide is a building block of a nucleic acid. A template is an existing sequence that guides construction of a complementary sequence. The symbols 5′ and 3′ are read five prime and three prime; they identify chemically different strand ends. Every short sequence and numerical example here is constructed for explanation unless identified as historical evidence.

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By the end, you can

Read a paired DNA sequence with its strand ends, and distinguish a DNA molecule from its changing chromosome packaging.

Distinguish the chain from the paired information

A DNA nucleotide contains a deoxyribose sugar, a phosphate group and a base. The four standard bases are adenine, thymine, guanine and cytosine, abbreviated A, T, G and C. Nucleotides join through covalent phosphodiester links to form a sugar–phosphate backbone. The order of bases along the chain records a sequence.

In a usual DNA double helix, the bases point inward and the backbones lie outside. A pairs with T, and G pairs with C. Hydrogen bonding contributes to the specificity of pairing, and interactions between stacked bases also help stabilise the structure. The covalent links within a backbone and the interactions between paired strands have different roles.

Complementarity means that one standard base sequence specifies the partner sequence. A change in order changes the stored sequence even if the total counts of A, T, G and C stay the same. A bag containing the correct letters cannot reveal their original order; counts alone therefore do not recover hereditary information.

Read the ends before reading the letters

The numbers 5′ and 3′ refer to positions in the nucleotide's sugar. They identify chemically different ends of a strand, rather than its fifth and third bases. The paired strands run antiparallel: following one from 5′ to 3′ follows its partner from 3′ to 5′.

The diagram shows 5′–ATGCC–3′ paired with 3′–TACGG–5′. Vertically aligned letters are complementary. By convention, a standalone DNA sequence is usually written from 5′ to 3′. To report the lower strand that way, read it from right to left: 5′–GGCAT–3′. Complementing letters and reversing reading order are separate operations.

This flat ladder is a reading aid, not a claim that DNA stays straight. Its rungs stand for paired bases and its rails for backbones. A double helix twists in three dimensions. Strand ends and pairing remain meaningful when a diagram is rotated, folded or drawn with curved strands.

Complementarity includes strand direction

Original five-pair segment, drawn as a flat ladder for orientation. It omits helix twist, atomic geometry, base stacking and molecular dimensions. Backbone rails and pairing rungs must use distinct visual styles.

Read the diagram in words

Five vertically paired positions show upper ATGCC with 5′ at left and 3′ at right; the lower aligned row is TACGG with 3′ at left and 5′ at right. Separate backbone rails connect successive nucleotides within each row. Pairing rungs join A–T and G–C across rows. A second reading arrow runs right to left along the lower row to show its conventional sequence GGCAT.

Complementarity includes strand direction
Strand	Left end	Bases from left to right	Right end
Upper strand	5′	ATGCC	3′
Lower strand	3′	TACGG	5′

Complementary base pair
Paired position	Upper base	Lower base
1	A	T
2	T	A
3	G	C
4	C	G
5	C	G

Lower strand read 5′→3′: GGCAT

5 base pairs = 10 nucleotides

Covalently linked sugar–phosphate backbone

A chromosome is organised DNA

In a typical eukaryotic nuclear chromosome, a long linear DNA double helix associates with proteins. DNA wrapped around histone protein cores forms nucleosomes. Further organisation helps fit DNA into a nucleus and affects access to its sequences. Chromatin means this DNA-and-protein material; its arrangement can change without changing the DNA's base order.

An X-shaped chromosome drawing usually represents a condensed, replicated chromosome. Its two sister chromatids each contain a DNA double helix. The X is not the shape of one naked DNA molecule, and an unreplicated chromosome does not already have two identical sister chromatids waiting to be filled.

Many bacterial chromosomes are circular, but chromosome organisation varies among lineages and is not captured by an all-bacteria versus all-eukaryotes rule. Cells may also contain additional DNA molecules, such as plasmids or organelle genomes. Always identify which genome or chromosome a diagram represents before generalising its shape or packaging.

Packaging and replication describe different changes

Schematic with no size scale. An X may represent the condensed sister pair but must not be presented as a naked DNA molecule or the permanent shape of every chromosome. The packaging view is not a mandatory, fixed sequence of higher-order fibres.

Read the diagram in words

One panel zooms from a DNA double helix to DNA wrapped around histone cores, illustrating nucleosomes. A separate panel compares one unreplicated chromosome with a replicated chromosome containing two sister chromatids, each explicitly labelled as carrying one DNA double helix. The zoom is a change of viewing scale; the replication arrow is a copying process and must look different.

View DNA packaging at another scale

DNA double helix: Two complementary strands form one molecule.
Histone core: DNA wraps around the protein core.
Nucleosome: Wrapped DNA and histone core.
Unreplicated chromosome: One chromatid containing a DNA double helix.
Sister chromatid A: Contains a DNA double helix after replication.
Sister chromatid B: Contains a DNA double helix after replication.

Packaging and replication describe different changes
From	To	Relationship
DNA double helix	Nucleosome	DNA wraps around histones
Histone core	Nucleosome	Protein core
Unreplicated chromosome	Sister chromatid A	DNA replication
Unreplicated chromosome	Sister chromatid B	DNA replication

Two sister chromatids form the replicated chromosome

Typical eukaryotic nuclear chromosome

Worked example

Check a proposed partner strand

For the constructed strand 5′–ATGCC–3′, first write the aligned complementary letters TACGG. The partner's left end must be 3′ and its right end 5′, giving 3′–TACGG–5′. If both aligned rows were labelled 5′ on the left, they would contradict antiparallel pairing.

To list the partner as its own conventional sequence, reverse the reading direction: 5′–GGCAT–3′. This short segment contains five base pairs when paired, but ten nucleotides across its two strands. A length stated in base pairs counts paired positions, not both chains added together.

Check your understanding

What is the aligned partner of 5′–ACGTTA–3′, including both ends?
Show reasoning
3′–TGCAAT–5′. Reading that partner in its own 5′→3′ direction gives 5′–TAACGT–3′.
Does a double-stranded segment of 12 base pairs contain 12 or 24 nucleotides?
Show reasoning
It contains 24 nucleotides: one nucleotide in each strand at each of the 12 paired positions.
Does an X-shaped replicated chromosome contain one DNA double helix stretched around the X?
Show reasoning
No. Each sister chromatid contains a DNA double helix. The drawing represents a condensed, replicated chromosome and its organisation, rather than one naked molecule.

What to carry forward

DNA sequence, antiparallel strand ends and chromosome packaging describe different features; keeping them distinct makes copying diagrams readable.

References

Resources supporting this lesson’s explanations and examples.