The image on your left shows a short length of DNA. The atoms are shown as spheres and are coloured according to the type of atom. (Carbon: grey, Oxygen: red, Nitrogen: blue, Phosphorous: orange)

Moving Molecules

The best way to get an impression of the three dimensional shape of the DNA molecule is to watch it move. You can do this using the mouse. Try positioning the mouse over the DNA molecule on your left, holding down the left mouse button and dragging (in all different directions). Notice how the DNA appears in 3D when you are moving it.

If you want to look more closely at a particular part of the molecule you can press the "Shift" key on the keyboard, hold down the left mouse button and drag the mouse (up and down). This will allow you to zoom in and out. If you want to return the DNA to its original size and orientation press the following grey button .

Colouring Atoms

The current colour scheme is called CPK (named after three scientists,Corey, Pauling and Kultun). However sometimes different colour schemes are used. Oxygen and nitrogen are almost always in red and blue, but other but other colours can be used for carbon. Press this button to show carbon atoms in yellow or this one to show them in green. Use the following button to return to standard CPK colouring .

Often displaying all the atoms in CPK colouring is confusing. Instead colour is used to illustrate certain features of a structure. This can be illustrated by the following examples.

DNA consists of two separate strands that wrap round each other to form a helix. Pressing the next button will show this by colouring one strand green and the other yellow .

The next button will use colour to show that each strand of DNA consists of a series of bases (coloured yellow or green) attached to a backbone (coloured magenta) . This can be seen better if just one strand of the DNA is shown . You can keep moving the DNA around with the mouse to get a better look at the way in which the bases are attached to the backbone.

Representing Molecules

So far atoms have been shown in what is called "spacefill" representation, in which atoms are represented by spheres whose size is proportional to the size of the atom.

An alternative way of showing the shape of the molecule is the "surface" representation . Here the backbone is shown in magenta and the bases are shown in white. The smoothed surface gives a better impression of the overall shape of the molecule because not every atom is shown in detail.

Often it is useful to simplify the depiction of a molecule by just drawing its backbone . As you will see on page 3 this "backbone" representation is particularly useful when we are interested in the path of a long stretch of DNA. Another simple representation of DNA involves the backbone along with bars representing the bases .

If you return to the spacefill model of DNA . you will see that while it gives an impression of the overall shape of the DNA molecule, it is not clear which atoms are connected (bonded) to each other. This is easier to see using two other representations. The first is called "ball and stick" and shows atoms as small spheres connected together by rods . The second is even simpler and just shows the bonds between atoms. This is known as "wireframe" . These views make it much clearer that DNA consists of two strands wrapped round each other.

On this page you have learnt some of the different ways of representing molecules. To discover a bit more about how the structure of DNA is related to its function please click on the "Next" button below.