Complementary Base Pairing: Definition & Explanation

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  • 0:43 Composition of the DNA…
  • 1:55 Structure of the DNA Molecule
  • 3:13 Chargaff Rule 1
  • 4:11 Complementary Base Pairing
  • 6:10 It Doesn't Stop Here!
  • 7:30 Lesson Summary
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Lesson Transcript
Instructor: Natalia Caporale
Explore the composition and structure of DNA molecules. Learn how DNA molecules are composed of four different types of nucleotides that pair with each other in a very specific, complementary manner.


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 four 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 a polynucleotide (poly means many in Greek). There are four different kinds of nucleotides that make up DNA, each 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 four letters: A, C, G and T. If you were to 'read' a polynucleotide molecule, it would read something like 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 and 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 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.

Chargaff 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 Chargaff, an Austrian biochemist who emigrated to the U.S. during the Nazi era, was studying the actual composition of DNA. It was known that DNA consisted of A, G, T, C, but what Chargaff found was that the proportion of each of these bases in DNA was not random. In fact, across different animal species (from sea urchin to salmon, and so on), 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 Chargaff Parity Rule 1 and played a key role in Watson's and Crick's understanding of the structure of DNA.

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