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
Click on the link within the text to download the RasMol Script
You are looking at the structure of the
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
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
Now we are looking at the
and have colored the G and C differently so you can easily
see what is meant by propeller
Another characteristic of
B-DNA is the 2'endo sugar pucker.
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.
Last revision: October 11, 1996