21.10: DNA Base Pairing

Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,

1. the amount of adenine (A) is equal to the amount of thymine (T);
2. the amount of guanine (G) is equal to the amount of cytosine (C); and
3. the sum of purines, A and G, is equal to the sum of pyrimidines, C and T (i.e., A+G = C+T).

Later work by Watson and Crick revealed that in double-stranded DNA, A always forms two hydrogen bonds with T, and G always forms three hydrogen bonds with C. This base pairing maintains a constant width of the DNA double helix, as both A-T and C-G pairs are 10.85Å in length and fit neatly between the two sugar-phosphate backbones.

Base pairings cause the nitrogenous bases to be inaccessible to other molecules until the hydrogen bonds separate. However, specific enzymes can easily break these hydrogen bonds to carry out necessary cell processes, such as DNA replication and transcription. As a G-C pair has more hydrogen bonds than an A-T pair, DNA with a high percentage of G-C pairs will need the higher energy for separation of two strands of DNA than one with a similar percentage of A-T pairs.

Base Analogs as Medicine

Correct base pairing is essential for the faithful replication of DNA. Base analogs are molecules that can replace the standard DNA bases during DNA replication. These analogs are effective antiviral and anticancer agents against diseases such as hepatitis, herpes, and leukemia. Acyclovir, also known as Acycloguanosine, is a base analog of guanine and is commonly used in the treatment of the herpes simplex virus. The guanine part of Acyclovir pairs with adenine as usual during DNA replication; however, because it does not have a 3’ end of the nucleotide, DNA polymerase cannot continue forming base pairs, and replication terminates.

DNA resembles a twisted ladder. And the rungs of the DNA ladder are complementary pairs of nitrogenous bases. According to base pairing rules, adenine, a purine, pairs with thymine, a pyrimidine, with two hydrogen bonds. And guanine, a purine, appears with cytosine, a pyrimidine, with three hydrogen bonds. But why do purines always pair with pyrimidines?

Due to steric constraints, that is, spatial restrictions imposed by the sugar phosphate backbone of the DNA, only a 10.85 angstrom space is available for the base pairs in a DNA double helix.

Purines have a double ring structure. Therefore, two purines together will be too big to fit in this space. On the other hand, if we put two pyrimidines together, which contain only a single ring, the distance between them will be too large to form hydrogen bonds, which are approximately two angstroms long.

However, if we pair a purine and a pyrimidine together, they fit perfectly inside the DNA helix and are close enough to form hydrogen bonds. Hydrogen bonds can form when a hydrogen atom is approximately two angstroms away from an electronegative atom, such as oxygen or nitrogen.

Adenine has one hydrogen atom close to an oxygen and thymine. And thymine has one hydrogen close to a nitrogen and adenine. This leads to the formation of two hydrogen bonds.

Adenine cannot form hydrogen bonds with cytosine, because cytosine has a hydrogen atom where the oxygen and thymine would be. And the hydrogen atom that is present in thymine is absent in cytosine.

A similar phenomenon occurs in the guanine cytosine base pair where an oxygen in guanine, and an oxygen and a nitrogen in cytosine are each positioned across from a hydrogen, leading to the formation of three hydrogen bonds, which does not happen in guanine thymine base pairing.

The high specificity of base pairing, along with the help of DNA replication enzymes, is why adenine always pairs with thymine and guanine always pairs with cytosine.