DNA Double Helix

An interactive tutorial for 162.101, Biology of Cells

Chime scripting by John Tweedie
©Copyright John Tweedie & Massey University, 2000, 2001, 2002, 2003

This is an interactive tutorial to allow you to manipulate the way thatthe DNA helix is displayed. In this way you will be able to get some idea of the 3-dimensional form of the structure. Once you have worked out how touse the interactive aspects of the software you can experiment as much as you like!

If you find this text is too small for you to read without strain you should use the browser controls to increase the displayed font size. If you are using Netscape Navigator, use the View menu to increase the size. (You may have to do this several times to see an effect.)

When the DNA molecule displayed in the frame to the left has stopped rotating click on the first button (box with an X in it) below. This will reload the file of structural co-ordinates and display the output inthe structure frame (black area to the left of the screen).

This structure shows a short fragment (13 base-pairs) of double-helical DNA. The two strands are shown in two shades of cyan (light & dark) with the hydrogen bonds between the base-pairs shown in white.
T he 3D effect is easier to see if the molecule is rotating. If you hold down the mouse button (right button on Windows-based computers) when the pointer is in the structure frame a pop-up menu will appear. Move the pointer down to the Rotation command and release the button. The molecule will rotate about the Y axis. To turn off the movement go to the pop-up menu and release the button when the pointer is on the Rotation command.
The next button will change the representation of the structure to highlight the atoms making up the backbone of the two strands.

In this representation the carbon atoms of the backbone are light grey, oxygens are red and phosphorus is gold. If you turn on rotation again the 3D nature of the structure will be clearer.

In this tutorial you can get unexpected results if you click on buttons in the wrong order. If this happens go back to the last large buttonyou clicked on.

The next button will change the size of the backbone atoms to indicate the electronic shells of the atoms (spacefilling representation) which gives a truer picture of the structure. Leave rotation on and click on the next button.

Turn the rotation command off now. (Use the pop-up menu in thestructure frame and go down to the rotation command.)
The button below will show the atoms of the bases in representativecolours. Carbon is light grey, oxygen red and nitrogen light blue.

Note the way in which the base-pairs are 'stacked' in a parallelarray of planar molecules. The plane of the base pairs is approximately at right angles to the axis of the helix.
This representation may give the impression that there is a lot of space between adjacent base-pairs. However the next button will change the view to show the atoms of the bases as spacefilling.

The next button shows the backbone atoms in spacefilling mode as well as the base-pairs. All of the atoms (base-pairs and backbone) are now shown intheir representative colors.

Base Pairs in DNA

So far we have only looked at the overall structure. Now we will concentrate on the base-pairs. The purine bases in DNA are adenine & guanine and the pyrimidines are cytosine and thymine. Click on the next button to display the double-helix with the bases colour coded:

Thymine (T)
Adenine (A)
Guanine (G)
Cytosine (C)
If the Rotation comand is turned on you should be able to see the arrangement of the base-pairs better.
Turn Rotation off before going to the nextsection.

A-T Base Pair

The next button will display an A-T base pair.

In this view the A-T base pair is shown from a view at right angles to the helix axis so we are looking at the edge of the base pair. The atoms are coloured according to their type (hydrogens are white) and the atoms of the backbone chain are not shown. Note that all of the atoms of the bases are in the same plane except the hydrogens of the methyl group of Thymine. The next button will rotate the structure through 90o so the view is down the helix axis.

In this view the shape of the base pairs is more apparent. Note the two hydrogen bonds between the bases. One is between one of the ring nitrogens of adenine (acceptor) and a hydrogen attached to a ring nitrogen of thymine (hydrogen bond donor). The second is between one of the hydrogens of the NH2 group of adenine (donor) and the keto oxygen of thymine (acceptor).
The next button adds the deoxyribose pentose sugars and the phosphate groups to the base-pairs. These groups form part of the backbone of the two DNA single chains which form the double helix.

In this view the deoxyribose groups are at right angles to the bases so you are looking from the edge of the pentose ring. The next button will change the colour of the carbon atoms of the pentose ring to green so they are more obvious.

Note that the bonds joining the two bases of the base pair to the deoxyribose sugars are not directly opposite each other. They form an angle so the the sugars and the phosphates are displaced to the top of the screen.
The next button will rotate the A-T base pair so the the view is from theside of the helix.

Now the deoxribose ring is more obvious. Note the orientation of the two rings (look at the red oxygen atoms in the deoxyribose rings). This isbecause of the opposite polarity of the two backbone chains of the DNA strands. Note also that this polarity is reflected in the way in which thephosphate groups are attached to the deoxyribose sugars.

G-C Base Pair

The next button will display a G-C base pair.

Once again the base-pair is displayed so that the view is from the side of the helix. The next button will rotate the display by 90o so that the view is down the helix axis.

In the G-C base pair there are three hydrogen bonds connecting the bases. Note which atoms form the hydrogen bond acceptors and donors. Click on the next button to add the deoxyribose sugars and the phosphate groups.

The deoxyribose ring atoms have not been highlighted in this view but you should still be able to see the pentose ring. Note again the asymmetry ofthe bonds between the bases and the deoxyribose groups of the DNA backbone. The next button will rotate the structure so that the view is from the side and the deoxyriboses can be seen more clearly.

Look at the way in which the backbone groups (deoxyribose and phosphate) have opposite polarity in the two chains.

Representation of Hydrogens in X-rayStructures

The structural representations of the A-T and G-C base pairs are derived from theoretical structure files in which the hydrogen atoms are shown. However most macromolecular structures such as DNA and protein molecules are determined by X-ray crystallography. This proceedure does not usually have sufficient resolution to determine the positions of the hydrogen atoms and they are usually omitted from the displayed structures. However when you are looking at the structures in the rest of the tutorial you should be aware that the hydrogens are missing. If you dont make this mental adjustment you are likely to be confused by the hydrogen bonds in the base pairs. To show this effect the next button will dispay an A-T base pair with the hydrogens shown.

Use the pop-up menu and go the the Options command and click the Display Hydrogens command. This should hide the hydrogens. Note that now the hydrogen bonds linking the bases appear to be directly between either two nitrogens or a nitrogen and an oxygen. This is of course chemically impossible. However you need to get used to this representation and mentally add the hydrogens. You should be able to use the Options menu to turn the hydrogens back on again. However there is a fault in the software which often makes the whole structure disappear when this is done. If this happens click the last button to restore the structure with hydrogens.
Note that display of the double helix in this tutorial also shows thehydrogens. This is because the structure file was generated bycomputer from the parameters of the Watson-Crick double helix structureand the hydrogens were included.

Putting the Base-Pairs into the Double Helix

The button below will display an adjacent G-C and A-T base pair in theDNA helix structure.

The bases are shown in the same colours as in the double helix shownearlier. The next button will rotate the display so the view is along thehelix axis.

This representation shows clearly the 36o rotation between adjacent base-pairs in the DNA. It also shows that the two base pairs predicted by Watson and Crick both fit nicely into the dimensions of the double helix. The button below will rotate the helix about its axis and you should see that the backbone groups of each base-pair describe a circle of the same radius.

The next button will change the view so you are looking from the side of the helix again.

Once again this stick representation might suggest that there is a greatdeal of space between the atoms in the base-pairs. The next button will change the atom representation of the bases to space filling with the size of the atoms approximating their electronic radii.

The next button will show the whole 13 base-pairs of this small DNAmolecule looking along the helix axis.

If you place the mouse pointer in the structure frame and move the mouse as you hold the button (PC's left button) down you can grab the structure andmove it yourself. Do this and rotate the DNA molecule to give different views. The more experimentation you do the more familiar you will become with the structure. In some views the ends of the DNA molecule will be off the screen. If you hold down the shift key while grabbing the structure with themouse button (lefty button) you can zoom in and out. Holding down the option key while grabbing the structure allows you to move the structure in the plane of the screen without rotating it.
There are also plenty of options in the pop-up menu box that appears in the structure window when you hold down the mouse key without moving the mouse. If you get lost you can always restore the structure by returning to the last button large button that you pushed.

I hope you enjoyed the tutorial. If you have any comments you would like to make which might improve the presentation and your understanding, could you please let us know. A short note to me through your lab. supervisor wouldbe fine or you can e-mail me at:

j.tweedie@massey.ac.nz

Use this link to return to the BiochemistryTeaching Group Tutorial page.

References & Acknowledgements

The DNA structure shown was generated from the sequence of the central 13base-pairs of the lac operator sequence using the utility programGenerate PDB Display from Text Input available from thePittsburg Supercomputing Center at thePSC WebTools page.