The Structure of DNA: The Double Helix

In 1953, a two-page paper in the journal Nature described a structure so elegant that its authors noted, almost in passing, that it “immediately suggests a possible copying mechanism for the genetic material.” The DNA double helix is one of the most recognisable shapes in science. Its beauty is not just visual: every feature of the structure has a chemical reason, and together they explain how DNA stores information and copies itself.

The ingredients

DNA is a polymer of nucleotides, each made of a deoxyribose sugar, a phosphate group and one of four bases: adenine (A), thymine (T), guanine (G) or cytosine (C). The nucleotides are joined by phosphodiester bonds into a strand with a sugar–phosphate backbone and a sequence of bases sticking out. (The chemistry of these parts is covered in nucleic acids: DNA and RNA chemistry.)

The double helix in five features

1. Two strands wound around each other

DNA consists of two strands coiled around a common axis into a right-handed double helix. If you look along the axis, the strands twist clockwise as they move away from you.

2. Backbones outside, bases inside

The sugar–phosphate backbones run along the outside of the helix, where their negatively charged phosphate groups are exposed to water and to positive ions. The bases point inwards, stacked like the steps of a spiral staircase, where their flat, largely non-polar ring surfaces are partly shielded from water.

3. Complementary base pairs

Each base on one strand pairs with a base on the other:

• A pairs with T, held by two hydrogen bonds;
• G pairs with C, held by three hydrogen bonds.

Each pair contains one purine (two rings) and one pyrimidine (one ring), so every “rung” of the ladder is the same width. That’s why A doesn’t pair with G (too wide) or C with T (too narrow). More detail in base pairing: A–T and G–C.

Because of this pairing, the two strands are complementary: if one strand reads 5′-ATGC-3′, the other must read 3′-TACG-5′. Knowing one strand tells you the other.

4. Antiparallel strands

The two strands run in opposite directions. One runs 5′→3′ from top to bottom; the other runs 3′→5′. This antiparallel arrangement is needed for the bases to line up correctly for hydrogen bonding, and it has major consequences for how DNA is copied (see DNA replication: the chemistry).

5. Major and minor grooves

The sugars attach to the base pairs asymmetrically, so the two backbones aren’t evenly spaced around the helix. This creates two grooves winding along the outside:

• the major groove, wide and deep;
• the minor groove, narrow and shallow.

The edges of the base pairs are exposed in the grooves, especially the major groove. Proteins that switch genes on and off “read” the DNA sequence by fitting into the major groove and forming hydrogen bonds with the exposed parts of the bases, without having to unwind the helix.

Dimensions of B-DNA

The common form of DNA in cells is called B-DNA. Its key measurements:

Feature	Value
Diameter	about 2 nm
Rise per base pair	about 0.34 nm
Base pairs per turn	about 10.5
Length of one turn (pitch)	about 3.4–3.6 nm
Handedness	Right-handed

Other forms exist. A-DNA is shorter and wider and forms when DNA is dehydrated. Z-DNA is a left-handed zigzag form adopted by certain sequences.

What holds the helix together?

It’s tempting to say “hydrogen bonds between base pairs”, but that’s only part of the story.

• Hydrogen bonds between complementary bases provide specificity: they make sure A pairs with T and G with C. Individually they’re weak, and water could offer bases alternative hydrogen-bonding partners, so they don’t contribute as much net stability as you might expect.
• Base stacking is the main source of stability. The flat bases stack on top of each other like a pile of coins, about 0.34 nm apart. They’re held by London dispersion forces and the hydrophobic effect, which drives the non-polar faces of the bases out of contact with water (see intermolecular forces).
• Cations such as Na⁺ and Mg²⁺ shield the negative charges on the phosphate groups, reducing repulsion between the two backbones.

Heating DNA separates the strands (melting or denaturation). The temperature needed rises with the proportion of G–C pairs, which have three hydrogen bonds and stack more strongly. When cooled slowly, complementary strands find each other and re-form the helix, a process called annealing, which is essential to PCR.

How the structure was discovered

By the early 1950s, scientists knew that DNA carried genetic information, and several key facts were known:

• Erwin Chargaff had found that in any DNA, the amount of A equals the amount of T, and G equals C (Chargaff’s rules), though the A+T to G+C ratio varies between species.
• At King’s College London, Rosalind Franklin and her student Raymond Gosling produced sharp X-ray diffraction images of DNA fibres. Her famous “Photo 51” (1952) showed a clear X-shaped pattern characteristic of a helix, and her measurements gave its key dimensions. She also established that the phosphate backbones lie on the outside.
• Maurice Wilkins, also at King’s, worked on DNA diffraction.

At Cambridge, James Watson and Francis Crick built physical models. Using Chargaff’s ratios, the dimensions from Franklin’s data (shown to them without her knowledge, which remains one of the most discussed ethical episodes in science), and careful thinking about the shapes of the bases, they realised that A–T and G–C pairs have the same overall size and could fit inside a double helix with antiparallel strands. Their model was published in April 1953, alongside papers from Wilkins’s and Franklin’s groups presenting the experimental evidence.

Watson, Crick and Wilkins received the Nobel Prize in Physiology or Medicine in 1962. Rosalind Franklin had died in 1958 and could not be included, since Nobel Prizes are not awarded posthumously. Her essential contribution is now widely recognised.

Why the structure matters

The double helix explains, in one picture:

• How information is stored: as a sequence of bases along a uniform backbone.
• How DNA is copied: each strand serves as a template for a new complementary strand.
• How information is protected: bases are tucked inside, and two copies of the information exist in every molecule, so damage to one strand can be repaired using the other.
• How genes are read: proteins recognise sequences through the grooves, and the strands can be temporarily separated to copy genes into RNA.

Key takeaways

• DNA is a right-handed double helix of two antiparallel strands.
• Sugar–phosphate backbones are on the outside; bases stack on the inside.
• A pairs with T (two hydrogen bonds) and G pairs with C (three hydrogen bonds), so the strands are complementary.
• The helix is stabilised mainly by base stacking, with hydrogen bonds giving pairing specificity and cations shielding the negative backbone.
• Franklin’s X-ray data, Chargaff’s rules and Watson and Crick’s model-building revealed the structure in 1953. Compare DNA with its cousin in DNA vs RNA.