Complementary base pairing describes the manner in which the nitrogenous bases of the DNA molecules align with each other. Complementary base pairings are also responsible for the double-helix structure of DNA. If you imagine yourself looking at a closet with 4 pairs of shoes that are all mixed up, complementary base pairing would be the set of rules that you would use to know which shoes go together. In a similar way to which only the correct two shoes will form a working pair (you don't want two left shoes, or a black and a brown one!), only some of the nitrogenous bases of DNA can interact to form a stable DNA molecule. Composition of the DNA Molecule DNA or deoxyribonucleic acid, is an amazing molecule that stores all of the genetic information of an organism. You might have heard that DNA is a polymer, that is to say, a molecule made of the many smaller subunits called monomers. In the case of DNA, the monomers are called nucleotides and the polymer is usually called polynucleotide (poly means many in Greek). There are four different kinds of nucleotides that make up DNA, each of them with one of four possible nitrogenous bases: adenine (A), cytosine (C), guanine (G) and thymine (T). You can think of polynucleotides as strings of words consisting of combinations of just 4 letters: A, C, G and T. If you were to 'read' a polynucleotide molecule, it would read: AGTCGCCTAGGC?etc.
Structure of the DNA Molecule
When people first realized that DNA contained all of our genetic information, they became very interested in understanding how it was organized/structured. While it was known that the DNA molecule contained two polynucleotide molecules, no one knew how they were organized together. Some people believed that they interacted through the phosphate part of the nucleotides, while others thought that they interacted through the bases. You can think of the DNA molecule being a zipper, with each DNA strand being represented by one strip of fabric. If you had never seen a zipper and someone gave you the two strips separated, how would you know if they normally attach to each through the 'metal teeth' (the bases in our case) or through the straight side of the fabric strip (the phosphates)? In 1953, Watson and Crick showed that the DNA molecule consists of two polynucleotide molecules that stand 'face to face' against each other, interacting at the level of the nitrogenous bases. If we go back to our zipper analogy, the two strands in DNA attach to each other through the nitrogenous bases in a similar manner to which the two strips of fabric in the zipper interlock to each other through the small metal pieces.
DNA strands of DNA interlock like the two strips of a zipper Chargraff Rule 1: More Insight into the Structure of DNA While Watson and Crick worked on the problem of the structure of the DNA molecule, Erwin Chargraff, an Austrian biochemist who emigrated to the US during the Nazi era, was studying the actual composition of DNA. It was known that DNA consisted of A, G, T, C, but what Chargraff found was that the proportion of each of these bases in DNA was not random. In fact, across different animal species (e.g., sea-urchin, salmon, etc.), he found that the number of As in the DNA was always equal to the number of Ts in the DNA and the number of Gs was equal to the number of Cs. This rule (%A = %T and %G = %C) is known as Chargraff Parity Rule 1 and played a key role in Watson and Crick's understanding of the structure of DNA (see image below).
Chargraff Rule 1 Complementary Base Pairing in The DNA Molecule When working on the structure of DNA, Watson and Crick not only figured out that the two polynucleotides in the DNA (i.e., the DNA strands) interacted through the bases, they also deduced, with the help of Chargraff's rules, that the bases were pretty picky as to whom they interacted with. Nucleotides containing Adenine (A) would only interact with nucleotides containing Thymine (T), while nucleotides containing Cytosine (C) would only interact with nucleotides containing Guanine (G). This meant that only two kinds of base pairs were possible: GC (or CG) and AT (or TA). So, the two strands of DNA are said to 'complement each other'. This is what we call complementary base pairing. Complementary base pairing explains Chargraff's findings. As Adenine always associates with Thymine, the number of As and Ts in DNA must always be the same. You can remember which base associates with which by using the mnemonic GCAT.
DNA molecule fragment (hydrogen bonds can be seen between the bases)