5.04: Base Pairing in DNA and RNA

Rules of Base Pairing

Two chemical diagrams of Watson-Crick DNA base pairs, with base names in red. Top pair: Thymine (left, a single six-membered pyrimidine ring bearing an H3C methyl group, two C=O carbonyls, and ring nitrogens) faces Adenine (right, a purine of a six-membered ring fused to a five-membered ring bearing an NH2 group). Two horizontal dotted lines represent hydrogen bonds between them: one from thymine's carbonyl oxygen to adenine's N???H, and one from thymine's N???H to adenine's ring nitrogen. Bottom pair: Cytosine (left, pyrimidine with an NH2 group and a carbonyl) faces Guanine (right, purine with a carbonyl and an NH2 group). Three horizontal dotted lines show hydrogen bonds: cytosine N???H to guanine carbonyl oxygen, cytosine ring nitrogen to guanine N???H, and guanine N???H to cytosine carbonyl oxygen. Individual atoms are labeled H, C, N, and O throughout. A short arrow points downward from the bottom of each of the four bases, indicating the bond to the sugar-phosphate backbone. The diagrams illustrate why A pairs only with T (two bonds) and C only with G (three bonds).

The rules of base pairing (or nucleotide pairing) are:

• A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T)
• C with G: the pyrimidine cytosine (C) always pairs with the purine guanine (G)

This is consistent with there not being enough space (20 Å) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. But why not A with C and G with T? The answer: only with A & T and with C & G are there opportunities to establish hydrogen bonds (shown here as dotted lines) between them (two between A & T; three between C & G). These relationships are often called the rules of Watson-Crick base pairing, named after the two scientists who discovered their structural basis.

The rules of base pairing tell us that if we can "read" the sequence of nucleotides on one strand of DNA, we can immediately deduce the complementary sequence on the other strand. The rules of base pairing explain the phenomenon that whatever the amount of adenine (A) in the DNA of an organism, the amount of thymine (T) is the same (called Chargaff's rule). Similarly, whatever the amount of guanine (G), the amount of cytosine (C) is the same. The C+G:A+T ratio varies from organism to organism, particularly among the bacteria, but within the limits of the experimental error, A=T and C=G.