DNA Structure — The Double Helix

DNA is the universal hereditary molecule of life. Its structure, solved by James Watson, Francis Crick, Rosalind Franklin and Maurice Wilkins in 1953, is one of the greatest discoveries in biology. This lesson covers the OCR A-Level Biology A specification point 2.1.3 (c) — the structure of DNA — including the antiparallel nature of the two strands, complementary base pairing, hydrogen bonding and the double helix itself.

A detailed understanding of DNA structure is essential not only for this topic but also for genetics, mutations, gene expression and genetic technologies in Year 2.

1. Historical Context (Non-Specification, Useful Background)

In 1953, Watson and Crick proposed the double-helical model of DNA based in large part on X-ray diffraction images taken by Rosalind Franklin and Maurice Wilkins at King's College London.
Erwin Chargaff had already shown that in any DNA sample, the amount of A equals the amount of T, and the amount of C equals the amount of G. This became known as Chargaff's rules.
The model elegantly explained how DNA could store information and how it could be copied accurately — the two central functions of a hereditary molecule.

Exam Tip: You do not need the historical detail for marks, but mentioning Chargaff's rules (A=T, C=G) in an answer about base pairing can show depth of understanding.

2. Overall Architecture

DNA is a double-stranded polynucleotide arranged as a right-handed double helix. Each strand is a polymer of nucleotides joined by phosphodiester bonds (see Lesson 1). The two strands wind around a common axis like a twisted ladder.

The main structural features are:

Two polynucleotide strands running antiparallel to one another
Sugar–phosphate backbone on the outside (polar, hydrophilic)
Nitrogenous bases on the inside, paired by hydrogen bonding
Complementary base pairing: A pairs with T, C pairs with G
A right-handed double helix with approximately 10 base pairs per turn
The helix contains a major groove and a minor groove (protein binding sites)

5' → 3' strand	Base 1	Base 2	Base 3	Base 4	3' → 5' strand
—P—S—	A (= T, 2 H-bonds)	T (= A, 2 H-bonds)	G (≡ C, 3 H-bonds)	C (≡ G, 3 H-bonds)	—S—P—
3' → 5' strand	Base 1	Base 2	Base 3	Base 4	5' → 3' strand
—S—P—	T	A	C	G	—P—S—

Key: S = deoxyribose sugar, P = phosphate, = denotes 2 hydrogen bonds (A–T), ≡ denotes 3 hydrogen bonds (G–C). The two strands run antiparallel; bases pair across the central axis of the helix.

3. The Antiparallel Strands

The two strands of DNA run in opposite directions: one runs 5' → 3' while the other runs 3' → 5'. This is what is meant by "antiparallel".

Strand	Direction	Base 1	Base 2	Base 3	Base 4
Strand 1	5' → 3'	A	T	G	C
Strand 2	3' → 5'	T	A	C	G

The vertical alignment indicates base pairing: A–T, T–A, G–C, C–G across the antiparallel strands.

Why antiparallel?

It allows the bases on each strand to align so they can form stable hydrogen bonds.
It enables the enzymes of replication and transcription to recognise and move along the strands in the correct direction.
DNA polymerase can only add nucleotides to the 3' end of a growing strand — so one strand is synthesised continuously and the other discontinuously during replication (see Lesson 4).

Exam Tip: When drawing DNA, always label the 5' and 3' ends and make sure they are on opposite ends of the two strands.

4. Complementary Base Pairing

The bases project inwards from the sugar–phosphate backbones and pair via hydrogen bonds according to strict rules:

Pair	Bonding	Hydrogen bonds
Adenine – Thymine (A–T)	Purine–pyrimidine	2 hydrogen bonds
Cytosine – Guanine (C–G)	Purine–pyrimidine	3 hydrogen bonds

Key consequences of this pairing:

A purine always pairs with a pyrimidine, keeping the width of the helix constant at approximately 2 nm. Two purines would be too wide; two pyrimidines would be too narrow.
C–G pairs are more stable than A–T pairs because three hydrogen bonds are stronger than two. DNA that is rich in G and C has a higher melting temperature.
Complementary base pairing means that if you know the sequence of one strand, you automatically know the sequence of the other. This is the basis of accurate DNA replication.

Key Definition — Complementary base pairing: The specific pairing of adenine with thymine (two hydrogen bonds) and cytosine with guanine (three hydrogen bonds) by hydrogen bonding between the bases in double-stranded DNA.

5. Hydrogen Bonds — Weak but Collectively Strong

Each individual hydrogen bond is weak, but a typical gene contains thousands of base pairs — so collectively, the double helix is held together by hundreds of thousands or millions of hydrogen bonds. This gives DNA two apparently contradictory properties:

Stability — the strands do not come apart spontaneously at body temperature.
Accessibility — enzymes can, when needed, separate the strands locally (e.g. DNA helicase during replication) without breaking strong covalent bonds.

The sugar–phosphate backbone, by contrast, is held together by covalent phosphodiester bonds, which are strong and do not break during replication or transcription.

graph TD
  A[Double helix] --> B["Sugar-phosphate backbone<br/>covalent phosphodiester bonds<br/>strong and permanent"]
  A --> C["Base pairs<br/>hydrogen bonds<br/>weak individually, strong collectively"]
  C --> D[A=T: 2 H-bonds]
  C --> E[C≡G: 3 H-bonds]

6. The Double Helix

The two strands twist around one another to form a right-handed double helix with the following dimensions (B-form DNA):

Diameter: ≈2 nm (20 Å)
Rise per base pair: 0.34 nm
Pitch (length of one complete turn): ≈3.4 nm
Base pairs per turn: ≈10
Major and minor grooves wind along the outside

You will not be asked to memorise the numbers, but mentioning "10 base pairs per turn" or "right-handed helix" adds precision to extended-answer questions.

7. How DNA Structure Relates to Function

DNA is often described as the molecule that is "perfectly suited to its function". Each structural feature can be linked to a specific function:

Structural feature	Related function
Sugar–phosphate backbone on the outside	Protects the genetic information (bases) from chemical damage; polar and soluble in the aqueous environment.
Bases on the inside of the helix	Bases are hydrophobic and shielded from water; base stacking stabilises the helix.
Double-stranded, complementary	Each strand is a template for the other — accurate replication and repair are possible.
Weak hydrogen bonds between bases	Strands can be separated for replication/transcription without breaking the backbone.
Strong phosphodiester bonds in the backbone	Confer overall chemical stability and resistance to mechanical stress.
Very long molecule	Can store vast amounts of information (≈3.2 billion base pairs per human haploid genome).
Double helix	Compact — enables coiling with histones and packaging into chromosomes.

Exam Tip: Questions often ask you to relate the structure of DNA to its function. Learn the table above and include specific structural features with specific functions — not vague statements like "it is stable".

8. Common Exam Mistakes

Drawing the two strands running in the same direction (parallel). They must be antiparallel — mark the 5' and 3' ends on opposite corners.
Forgetting to say that the hydrogen bonds are between the bases, not between the strands generally.
Writing "A pairs with C" or similar wrong pairings. Always: A–T (2 H-bonds), C–G (3 H-bonds).
Saying "covalent bonds" hold the two strands together. The two strands are held by hydrogen bonds between bases. Covalent bonds (phosphodiester) are within each strand.
Calling DNA a "single helix" or "double strand" — it is a double helix of two antiparallel polynucleotide strands.
Saying that C–G bonds are "stronger" in a vague sense. Specify: three hydrogen bonds versus two.

9. Exam-Style Questions

Describe the structure of DNA. (6)
Explain why the two strands of DNA are described as "antiparallel". (2)
Explain how the structure of DNA allows it to carry out its functions. (6)
State two differences between the bonds holding the two strands together and the bonds within each strand. (2)

Model answer for (2): "The two strands run in opposite directions. One strand runs 5' to 3' and the other runs 3' to 5'. This antiparallel arrangement allows complementary base pairing between the two strands."

Summary

DNA is a double-stranded polynucleotide forming a right-handed double helix.
The strands are antiparallel (5'→3' alongside 3'→5').
The sugar–phosphate backbone is on the outside; the bases are on the inside.
Complementary base pairing: A–T with 2 H-bonds, C–G with 3 H-bonds.
Hydrogen bonds are individually weak but collectively strong — perfect for a molecule that must be both stable and accessible.
Every structural feature of DNA can be linked to its functions: information storage, accurate replication and efficient packaging.

A-Level Deep Dive

Spec mapping

Spec Mapping: This lesson is mapped to OCR H420 Module 2.1.3 — Nucleotides and nucleic acids, covering the structure of DNA, complementary base pairing, antiparallel polynucleotide strands and the double helix (refer to the official OCR H420 specification document for exact wording).

DNA structure is the spine of OCR Module 2.1.3 and the conceptual foundation for replication (Lesson 4), transcription (Lesson 6), translation (Lesson 7), the inheritance topics of Module 6.1, the meiosis content of Module 5.1.5, and the gene-technology topic of Module 6.1.3. Examiners can ask about DNA structure on Paper 1, Paper 2 and Paper 3 — and synoptically as part of any extended-response question on cell division, gene expression or genetic engineering. The detail of antiparallel strands, complementary base pairing and the major/minor groove are recurrent assessment objects.

Scientists and paradigms

The double-helix model is one of the most well-documented scientific stories of the twentieth century, but for exam purposes you need only the schools of thought, not invented quotations.

Erwin Chargaff (1950): in any DNA sample, %A = %T and %C = %G. These ratios are now known as Chargaff's rules, and they were a major geometric clue — they told whomever could read them that DNA's two strands were complementary, not random.

Rosalind Franklin and Maurice Wilkins (King's College London, 1951–1953): used X-ray diffraction of fibres of crystalline DNA to obtain the diffraction pattern known as "Photograph 51". The pattern's central X-shape diagnosed a helical structure, and the spacings encoded both the helix's pitch (3.4 nm per turn) and the rise per base pair (0.34 nm). Franklin's measurements and her insistence on the B-form geometry of hydrated DNA were the load-bearing experimental data.

James Watson and Francis Crick (Cavendish Laboratory, Cambridge, 1953): combined Franklin's diffraction data, Chargaff's base ratios, and Pauling's α-helix model-building technique to propose the right-handed double-helix model with two antiparallel strands held together by hydrogen-bonded A–T and C–G base pairs. They were awarded the 1962 Nobel Prize in Physiology or Medicine together with Wilkins. Paraphrase the school of thought — do not invent dialogue. The model's predictive power was immediate: it suggested semi-conservative replication (Meselson & Stahl, 1958, see Lesson 4) and a template-based mechanism for transcription.

Synoptic links

This lesson connects forward to:

ocr-alevel-biology-nucleic-acids-enzymes — DNA replication (Lesson 4): semi-conservative replication is intelligible only because the two strands are antiparallel and complementary. Helicase exploits the relative weakness of hydrogen bonds; DNA polymerase III exploits the 5'→3' directionality.
ocr-alevel-biology-nucleic-acids-enzymes — Transcription (Lesson 6): the template strand is read 3'→5' to produce mRNA 5'→3' — a direct consequence of antiparallel geometry.
ocr-alevel-biology-genetics-inheritance — Mutations: substitution, insertion and deletion mutations are defined relative to the linear base sequence. Frameshift mutations are catastrophic because the reading frame is set by the 5' end of mRNA.
ocr-alevel-biology-genetics-inheritance — Gene technology: restriction endonucleases recognise specific palindromic sequences (themselves a consequence of complementary base pairing), and DNA ligase reseals the phosphodiester backbone you meet here.
ocr-alevel-biology-cell-structure: chromosome packaging — DNA wraps around histone octamers to form nucleosomes (~147 bp per nucleosome). Histone basicity (lysine, arginine) is electrostatically attracted to the δ⁻ phosphate backbone of this lesson.

Specimen question modelled on the OCR H420 paper format

Question (6 marks): Describe the structure of a DNA molecule.

Mark scheme decomposition (AO breakdown):

Lesson 2: DNA Structure — The Double Helix