Content area
Full Text
Almost all our students have heard that DNA is a double helix. This double helix provides a beautiful and easy-tounderstand example of how intermolecular forces combine to determine macromolecular structure. A simple consideration of hydrogen bonds, dispersion forces, and ionic interactions explains why DNA is most stable as a helix. A model easily made from boxes and string illustrates the principles clearly. I present this demonstration to my general chemistry students after intermolecular forces have been introduced. The model may also be used in more advanced classes to explain how intercalators, such as ethidium bromide, unwind DNA when they wedge between base pairs.
Introduction to DNA
To understand why DNA is helical, its components must first be described. DNA (deoxyribonucleic acid) is a polymer of nucleotides (Fig. 1). Each nucleotide contains phosphoric acid, the sugar deoxyribose, and one of four nitrogencontaining aromatic bases: thymine (T), adenine (A), cytosine (C), and guanine (G). The monomers are connected via ester linkages in which the phosphoric acid combines with the hydroxyl groups of the sugars. Each phosphate makes two ester linkages: one with the hydroxyl group on carbon three on one side of the deoxyribose, and one with the hydroxyl group of carbon five of the deoxyribose on its other side. The third acid group of phosphoric acid is very acidic and is fully dissociated under physiological conditions (neutral pH). The result is an alternating chain of sugars and phosphates with a negative charge on each phosphate. The bases are connected to carbon one of each deoxyribose and are found in the middle of the DNA structure. A more detailed description of the general structure of DNA can be found in any general chemistry or biochemistry text (1).
It is the order of the bases in the middle of the DNA molecule that gives DNA its ability to convey genetic information. To stress the importance of the bases, the structure of DNA is often abbreviated to show the sugar phosphate backbone as a simple line connecting the bases, as seen in Figure lb. We will see that this representation is also rational from a chemical point of view.
Intermolecular Forces Determine DNA Structure
Figure la shows the true complexity of DNA. There is potential for full or...