Why is DNA a helix?
Many people perceive the double helical structure of DNA (left) to
be an extremely elegant, and in some ways miraculous structure.
Clearly, the presence of two complementary strands is an efficient
solution to the problem of the replication of DNA - how to make two
exact copies from one original - but why is DNA helical?
In fact, as this short tutorial aims to show you, the helix is a
general response to the stacking up of single monomer units into a
polymer - DNA cant help being a helix.
This tutorial uses a utility called Jmol, which allows us
to manipulate 3-D structures. If you click and drag on the DNA
structure, you can rotate it around at will. Try it!
Helices are actually extremely common in macromolecules - the obvious example is the
in proteins, but there are many others:
- The helix of protein subunits in tobacco mosaic virus,
- The helix of α-helices in α-keratin,
- The triple helix of poly proline-glycine helices in
Even large stretches of
have a characteristic left-handed helical
twist when viewed edge-on.
So the question above might be recast as:
Why are helices so common in macromolecules?
We can address this question by simplifying the situation.
Consider the repeating units of a polymer (the nucleotides of DNA or
the amino acids of a protein) as building blocks.
Click here to see a
If you have rotated it, then click to reset it to its original
You can rotate the structure in the left-hand window at any time.
Now, lets stack another
on top. Then lets add
, with each block having the same relationship to the previous one. You will not be
surprised to see a simple stack of blocks!
However, the building blocks of macromolecules are in
general chiral, asymmetric, molecules, not regular rectangular
blocks. We can model this in a simple way by considering a
. Now we'll stack a
, as before. Adding
causes the stack to curve around, in this case into
But, there is no reason why the building blocks (monomers)
will stack on top of each other in a regular face to face way. There
is very likely to be some asymmetry in the way the blocks stack. Here
is the same
but this time the second block stacks onto it with a
Rotate the structure to get the idea.
If we now continue to add blocks with the same
, then we generate a helix.
So, it's really fairly easy to form a helix given some simple (and
realistic) rules about the way monomers (blocks) stack together. Of
course, to make a double helix, we can simply fill in the other
strand. Click for a
We can see the same thing with real DNA. Here is one
of DNA. Think of it as an asymmetric block, as before.
stacked on top. Continuing to add them with the same
relative orientation makes a helical
It would actually be difficult to arrange the
relationship of one nucleotide to the next, given the asymmetry of
the molecule, for repeated additions of nucleotide not to form
a helical structure. Finally, we can add the
Of course, the actual shape of DNA is determined by the allowed
bond angles in the sugar-phosphate backbone, the way the hydrophobic
bases stack together and the interaction between the two strands. The
simple model presented here is a not a substitute for this sort of
molecular explanation of the actual conformation of DNA, but
it explains why helical structures are so common. As you know, DNA
can adopt a variety of structures: A, B, Z (but crucially, they are
Coordinates of blocks were calculated by Andy Bates, using
Microsoft Excel and a hazy recollection of O-Level trigonometry.
Standard coordinates for a 12 bp double-stranded B-DNA
were created with the Biopolymer Module of the Biosym Insight II
software (version 95.0) running on a Silicon Graphics Indigo.
Thanks to Bill Primrose.
The α-helix structure is human apolipoprotein-E4, the collagen structure is that of a collagen-like peptide and the β-sheet structure is a mouse Fab antibody fragment
Block coordinates and Jmol scripts © A D Bates 2005, all rights reserved. Enquiries to Andy Bates.