Dickerson Dodecamer

To view and manipulate the following graphic images you will need to install RasMol 2.6. on your computer. See the instructions page for how to download and install this software.

Click on the link within the text to download the RasMol Script

You are looking at the structure of the Dickerson Dodecamer as determined by X-ray crystallography. The sequence of this piece of double-stranded DNA is as follows:

5' - CGCGAATTCGCG - 3' 3' - GCGCTTAAGCGC - 5'

The residues in each strand are numbered from 1 to 12 in the 5' to 3' direction.

As you go through this tutorial, you will look at a number of views of this molecule designed to highlight certain features. Feel free to experiment with the various menu options at any time.

You are now looking at a space-filling model of the dodecamer, with the atoms of the sugar phosphate backbone in the conventional CPK colors, and the atoms of the bases colored purple. The sugar phosphate backbones spiral around the outside of the molecule. The edges of the bases are visible in the major and minor grooves between the backbones. Clicking on the arrow on either side of the bottom scroll bar will rotate the molecule about the helical axis allowing you to appreciate the nature of the major and minor grooves.

Many processes in genetics require that proteins be able to recognize and bind to specific sequences of basepairs in double-stranded DNA. Since the bases are only accessible via the grooves, this is generally accomplished by H-bond and apolar contacts between the protein and certain features on the major and minor groove edges of the basepairs. In this view, the H-bond acceptors in the grooves have been colored yellow, while the H-bond donors have been colored green. The thymine methyl groups (the main surfaces in the grooves available for apolar contact with proteins) have been colored magenta. All a protein can sense when it is searching for a particular sequence is the spatial arrangement of these various H-bonding and apolar groups. Carefully examine the major and minor grooves at various points along the length of the molecule to get a feel for what it is that a protein sees when it is attempting to recognize a specific DNA sequence.

In this view of the dodecamer, one of the GC nucleotide pairs is highlighted. By zooming in on this basepair, we will be able to closely examine some of the structural features of B-DNA.
All nucleosides in B-DNA assume the anti glycosidic bond angle. See if you can get a good view of the glycosidic bond angle by rotating and translating the dodecamer.

Here we see a view in which we've eliminated everything except the G and C bases of the GC nucleotide pair. A characteristic of B-DNA is propeller twist in which the two bases in a basepair are rotated relative to one another so that they are not in the same plane.
Now we are looking at the basepair edge-on and have colored the G and C differently so you can easily see what is meant by propeller twist.

     Another characteristic of B-DNA is the 2'endo sugar pucker.
     Here we have eliminated everything from view but the deoxyribose of the C residue. See if you can rotate it to get a good view of the sugar pucker.
     In case you were not satisfied with your efforts to examine the sugar pucker, here is an appropriately rotated, magnified, and labeled view of the deoxyribose residue, which should make the sugar pucker very clear to you.

voh@chem.ucla.edu // Last revision: October 11, 1996