This DNA 3D model is built atom by atom from published B-DNA coordinates. Rotate it, click any part to see what it is, switch on labels for the phosphates, sugars, bases and hydrogen bonds, and compare the three forms DNA takes: A, B and Z.
What the DNA 3D model shows
The model shows 24 base pairs of B-DNA, the form found in living cells. That is a little over two full turns of the double helix. Every carbon, nitrogen, oxygen and phosphorus atom sits where X-ray crystallography puts it, so distances in the model are real distances. Hydrogen atoms are left out, as in most structural models, because they are too small to show at this scale.
The default sequence is CGCGAATTCGCG, the Drew-Dickerson dodecamer. In 1980 it became the first stretch of B-DNA solved as a single crystal, which confirmed the double helix Watson and Crick had proposed 27 years earlier.
Parts of DNA, labeled
DNA is a chain of nucleotides. Each nucleotide has three parts:
- A phosphate group: one phosphorus atom bonded to four oxygens. Phosphates carry a negative charge, which is why DNA is an acid. Show the phosphates.
- A deoxyribose sugar: a five-carbon ring. Its carbons are numbered 1′ to 5′, and those numbers give the strand ends their names. Show the sugars.
- A nitrogenous base: adenine (A), thymine (T), guanine (G) or cytosine (C). The order of the bases is the genetic code. Show a base pair.
Phosphates and sugars alternate to form the sugar-phosphate backbone on the outside of the helix. The bases point inward and stack on top of each other like the steps of a spiral staircase. Turn on Labels in the right-hand panel to name every part on the model, or use the Teacher tab to download a labeled DNA diagram.
The 3D structure of DNA in numbers
B-DNA is a right-handed double helix. These are its standard dimensions:
| Measurement | B-DNA |
|---|---|
| Helix diameter | about 2 nm (20 Å) |
| Rise per base pair | 0.34 nm |
| Base pairs per turn | 10 to 10.5 |
| Length of one turn (pitch) | 3.4 to 3.6 nm |
| Twist per base pair | about 34 to 36° |
| Major groove width | about 2.2 nm |
| Minor groove width | about 1.2 nm |
Fiber X-ray models use exactly 10 base pairs per turn. DNA in solution averages about 10.5, which is why textbooks give both figures. Switch on Measurements to see the diameter, one full turn and the rise drawn on the model.
Base pairing and hydrogen bonds
The two strands are held together by hydrogen bonds between bases. Adenine always pairs with thymine through 2 hydrogen bonds. Guanine always pairs with cytosine through 3 hydrogen bonds. Each pair joins a two-ring base (A or G, the purines) to a one-ring base (T or C, the pyrimidines), so every rung of the ladder has the same width and the helix stays a constant 2 nm across.
Because the pairing rule is fixed, one strand fully determines the other. That is how a cell copies its DNA: it separates the strands and builds a new partner for each one. Drag the Unzip the strands slider to pull the strands apart and watch the hydrogen bonds break. Hydrogen bonds are weak on their own, but a gene has thousands of them. Stacking forces between neighboring bases, a kind of van der Waals interaction, add most of the remaining stability.
Why the strands run in opposite directions
Each strand has a direction. One end carries a free phosphate on the 5′ carbon of its sugar (the 5′ end). The other end carries a free hydroxyl on the 3′ carbon (the 3′ end). The two strands of a double helix run in opposite directions, so the 5′ end of one strand lies beside the 3′ end of the other. This arrangement is called antiparallel, and it is the only way the bases line up for pairing. Turn on the 5′ and 3′ ends labels to see it.
Major and minor grooves
The two backbones do not sit evenly around the helix. The sugars of a base pair attach on the same side, so the gaps between the backbones alternate between a wide major groove and a narrow minor groove. The edges of the bases are exposed at the bottom of each groove. Proteins that switch genes on and off read the sequence through the major groove without opening the helix, because each base pair presents a distinct pattern of atoms there.
A-DNA vs B-DNA vs Z-DNA
DNA can take three main shapes. Use the Form tab to watch the model change between them.
| A-DNA | B-DNA | Z-DNA | |
|---|---|---|---|
| Handedness | Right | Right | Left |
| Diameter | about 2.3 nm | about 2 nm | about 1.8 nm |
| Base pairs per turn | 11 | 10 to 10.5 | 12 |
| Rise per base pair | 0.26 nm | 0.34 nm | 0.37 nm |
| Where it occurs | Dehydrated DNA, DNA-RNA hybrids | Most DNA in cells | Alternating C-G stretches under strain |
A-DNA is shorter and wider, with its bases tilted away from the axis. Z-DNA zig-zags because its guanines flip into an unusual orientation, and it only forms on sequences that alternate C and G. The model switches to a CGCG sequence when you choose Z-DNA.
How to make a DNA model for school
A physical DNA model follows the same rules as the 3D one:
- Pick four colors for A, T, G and C, plus one color each for sugars and phosphates. The color key in the Teacher tab works for beads, candy or paper.
- Build two backbones by alternating sugar and phosphate pieces.
- Attach a base to every sugar. Pair A only with T and G only with C.
- Point the two backbones in opposite directions and mark the 5′ and 3′ ends.
- Twist the ladder to the right, one full turn for every 10 rungs.
Pipe cleaners with pony beads, licorice with gummy candies and foam balls with toothpicks all work. Download the printable labeled diagram or the blank worksheet from the Teacher tab to check the finished model. For more project ideas, see these biology topics by grade.
Who discovered the structure of DNA
In May 1952, Raymond Gosling, a PhD student working under Rosalind Franklin at King's College London, recorded the X-ray image known as Photo 51. Its X-shaped pattern showed that DNA is a helix and gave its dimensions. Maurice Wilkins showed the image to James Watson without Franklin's knowledge. Watson and Francis Crick published their double helix model in Nature on 25 April 1953, in the same issue as papers by Wilkins and by Franklin and Gosling. Watson, Crick and Wilkins received the 1962 Nobel Prize. Franklin had died in 1958, and the prize is not awarded after death. Many scientists now call it the Watson-Crick-Franklin model to credit her data.
Frequently asked questions
What are the parts of DNA?
DNA is made of nucleotides. Each nucleotide has a phosphate group, a deoxyribose sugar and one of four bases: adenine, thymine, guanine or cytosine. Sugars and phosphates form the backbone, and paired bases form the rungs.
How wide is a DNA molecule?
B-DNA is about 2 nanometers wide. That is roughly 50,000 times thinner than a human hair.
How many base pairs are in one turn of DNA?
About 10.5 base pairs in solution, or 10 in the classic fiber model. One turn is about 3.4 to 3.6 nanometers long.
What holds the two strands of DNA together?
Hydrogen bonds between paired bases, 2 for each A-T pair and 3 for each G-C pair, plus stacking forces between neighboring base pairs.
Is DNA a right-handed or left-handed helix?
B-DNA and A-DNA are right-handed. Z-DNA is left-handed and forms only on certain sequences.
Can I use the DNA 3D images in class or on my website?
Yes. Images and printables from this page are free to use under CC BY 4.0 with credit to 33Science. The Teacher tab also gives an embed code for the interactive model.
Related on 33Science
Sources
- Alberts B. et al. Molecular Biology of the Cell, 4th ed., chapter 4, section "The Structure and Function of DNA." NCBI Bookshelf.
- Drew H.R. et al. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. PNAS 78:2179. PDB entry 1BNA.
- Watson J.D. and Crick F.H.C. (1953). Molecular structure of nucleic acids. Nature 171:737.
- King's College London. The story behind Photograph 51.
Credits and sources
- Atomic geometry: Coordinates rebuilt from wwPDB 1BNA (Drew et al. 1981, PNAS 78:2179), 440D (Gao, Robinson & Wang 1999, Eur. J. Biochem. 261:413), 1D78 (Thota et al. 1993, Acta Cryst. D49:282) and 2DCG (Wang et al. 1979, Nature 282:680); wwPDB data are CC0. Ideal helices: uniform twist and rise, mean crystallographic base-pair geometry.
- The model, labels and poster image are by 33Science, licensed CC BY 4.0. Credit 33Science and link to this page.