A DNA (Deoxyribonucleic acid) Hairpin Loop

DNA consists of a linear polymer consisting of three types of molecule: an organic aromatic flat base connected to 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.