A DNA (Deoxyribonucleic acid) Hairpin Loop
DNA consists of a linear polymer consisting of three types of
molecule: an organic aromatic flat base
a sugar called ribose,
with an inorganic phosphate linker.
Two (or sometimes three) of these linear
polymers associate via weak interactions called hydrogen bonds
to form a
double strand. The individual structures of the bases, ribose and phosphate
and the way the hydrogen bonds form, forces this double strand to adopt a helical shape
(the famous Watson-Crick double helix).
When this structure was discovered, the helical characteristics were
deduced from a technique known as x-ray crystallography. However, it is
possible to deduce the helix by other spectroscopic methods as well. One
of these is known as "NMR" (Nuclear Magnetic Resonance) spectroscopy. NMR
takes many forms, one of which monitors the hydrogens in the molecule, and
in particular only shows up pairs of hydrogens which are about 3.5Å or less
apart in space. Shown below is part of such a (NOESY) NMR spectrum for
a particular small DNA-like molecule known as a "hairpin loop". This is
different from normal DNA in that it only comprises a single strand of
the basic DNA polymer, but the two ends of this strand are said to be
self-complementary, and hence they associate into a partial double helix,
whilst the middle section of the strand bends over to form the "hairpin".
In the spectrum below (of a DNA polymer known as CGCGTTTTCGCG), each peak corresponds to a close contact between
one of the aromatic base protons and one of the ribose protons (the
so-called anomeric proton). In constructing a structure where these protons
are the requisite 3.5A or less from eachother, the only possible 3D model one
can come up with is a double-helix. In the display below, if you move
the mouse cursor above each peak in the spectrum, the particular labels
of the two protons involved will appear in the status window of your browser.
If you click on this selection in the list below the spectrum, these two
protons will appear highlighted in the 3D model of the hairpin loop shown.