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Molecular Biology · Nucleic acid

DNA Double Helix 3D Structure

Two strands of DNA wound round each other, held together by base pairs: twelve of them here, about one full turn of the double helix.

DNA keeps its information in the order of four bases along a sugar and phosphate backbone. Two strands run in opposite directions and pair base to base, A with T and G with C, so each strand carries what is needed to rebuild the other. This crystal structure, first reported in 1980 and refined in 1981, was the first to show a whole turn of B-DNA, the form found in cells.

Also called B-DNA or Deoxyribonucleic acid.

The DNA double helix standing upright: two grey sugar and phosphate backbones winding round the outside, with the stacked base pairs as rungs between them.
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A double helix of two strands

Two strands of DNA wind round each other in a right-handed helix about 2 nanometres across. The backbones run along the outside and the bases point inwards, where each pairs with a base on the other strand.

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View 1 of 7: A double helix of two strands

Download the pictureDownload the atoms (PDB)Checked against its sources on 25 October 2026.

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The DNA Double Helix structure, explained

  1. 01A double helix of two strands

    Two strands of DNA wind round each other in a right-handed helix about 2 nanometres across. The backbones run along the outside and the bases point inwards, where each pairs with a base on the other strand.

  2. 02Two strands, running opposite ways

    Each strand has a direction, from the 5′ end of its sugar chain to the 3′ end. The two run in opposite directions, so the 5′ end of one strand lies beside the 3′ end of the other. This is what antiparallel means.

  3. 03The backbone on the outside

    Each sugar is joined to the next through a phosphate, by phosphodiester bonds. With the phosphates on the outside, facing the water, DNA is a strongly negatively charged molecule, which is why it moves towards the positive pole in gel electrophoresis.

  4. 04A pairs with T

    Inside the helix each base pairs with one on the other strand. Adenine always pairs with thymine, through two hydrogen bonds, because only that pair has the right shape and the right donors and acceptors.

  5. 05G pairs with C

    Guanine pairs with cytosine through three hydrogen bonds. Every pair, A-T or G-C, is a larger purine opposite a smaller pyrimidine, so every rung is the same width and the helix stays even.

  6. 06Stacked like coins

    The flat base pairs stack about 0.34 nanometres apart, about ten to a turn. Stacking, more than the hydrogen bonds between the bases, is what holds the helix together. Twelve pairs make a little more than one full turn, as here.

  7. 07A sequence an enzyme can read

    The middle six bases, GAATTC, read the same on both strands. This is the site of EcoRI, a restriction enzyme that recognises this sequence by touching the edges of the bases in the major groove, then cuts it.

Parts

What each part does

Strand 1
Twelve nucleotides, CGCGAATTCGCG, read from its 5′ end to its 3′ end. Each nucleotide is a phosphate, a deoxyribose sugar and a base.
Strand 2
The same twelve bases, running the other way. Because the sequence reads the same on both strands, the two strands are identical: a palindrome.
Sugar and phosphate backbone
Deoxyribose sugars joined through phosphates by phosphodiester bonds. It runs along the outside of the helix, and its phosphates carry negative charges in water.
Bases
Adenine, thymine, guanine and cytosine, flat rings that stack on top of each other inside the helix. Their order along a strand is the genetic information.
A-T base pairs
Adenine pairs with thymine through two hydrogen bonds. The four in the middle of this piece, AATT on each strand, make the helix's narrowest stretch of minor groove.
G-C base pairs
Guanine pairs with cytosine through three hydrogen bonds. G-C rich DNA holds its two strands together more tightly than A-T rich DNA, partly from the extra bond and partly because G-C pairs stack more strongly on their neighbours.
EcoRI site
GAATTC on both strands: the sequence the restriction enzyme EcoRI recognises and cuts, between the G and the first A of each strand.

The structure

Where these atoms come from

Structure
PDB 1BNA
What it is
B-DNA dodecamer, 5′ CGCGAATTCGCG 3′
Organism
Synthetic
Method
X-ray diffraction, 1.9 Å resolution
Deposited
1981
Atoms shown
486, without water or hydrogens
Paper
Drew HR and others, Proc Natl Acad Sci U S A 1981

Coordinates from the Protein Data Bank, free of all copyright (CC0). Water and hydrogens are left out, and the molecule is turned to face you; every atom is where the experiment placed it.

Dictionary

The terms to know

Practise it

The quizzes and cards that fit

See it at work

Diagrams it belongs to

Next to it

More molecules

Sources

Where the facts come from

Written by biofideX from these sources. Drawn with 3Dmol.js (Rego and Koes, Bioinformatics 2015).

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