Watson and Crick Base Pairs

Core Concepts

In this biochemistry tutorial, we learn all about Watson and Crick base pairs, including their importance, structure, and chemistry, as well as some important non-Watson-Crick base pairs.

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What is the Watson-Crick Model of DNA?

In 1953, biochemists James Watson and Francis Crick published the first model of the DNA double helix. They were able to develop this now-famous model through the DNA imaging done by Maurice Wilkins and Rosalind Franklin using X-ray crystallography. The Watson-Crick model of DNA structure corresponded specifically to B-DNA, the most common DNA tautomer, and included many correct details:

The phosphates and sugars point outside while the nitrogenous bases remain paired inside the helix, resulting in a “twisted ladder”
The antiparallel orientation of the strands (3’-5’ and 5’-3’)
The existence of major and minor grooves
The right-handed, clockwise twist of the DNA

By far the most groundbreaking detail of the model was the pairing of nitrogenous bases, appropriately named Watson-Crick base pairing. Considered a staple of DNA biochemistry, Watson-Crick base pairing involves Adenines pairing with Thymines and Guanines pairing with Cytosines. Or, as biology students often memorize: A’s with T’s, G’s with C’s.

For their work, Watson and Crick shared the 1962 Nobel Prize in Physiology and Medicine with Maurice Wilkins. Rosalind Franklin was not credited with the 1962 prize for her contribution.

The Structure of Nitrogenous Bases in Watson-Crick Base Pairs

The four nitrogenous bases in DNA have can be divided into two groups:

Pyrimidines: Thymine and Cytosine
Purines: Adenine and Guanine

In organic chemistry, pyrimidine is a benzene-like aromatic ring with two nitrogens at positions 1 and 3. As derivatives of pyrimidine, thymine, and cytosine have unique substituents attached to the ring structure. Cytosine has an amino group attached to Carbon 4 and a carbonyl at Carbon 2. Conversely, thymine has two carbonyls at Carbons 2 and 4 as well as a methyl group at Carbon 5. Uracil, the RNA equivalent of thymine, also counts as a pyrimidine, with the same structure as thymine minus the methyl.

pyrimidines capable of watson-crick base pairs

uracil capable of watson-crick base pairs

Contrastingly, purine is a nine-membered aromatic double ring involving four nitrogen heteroatoms at positions 1, 3, 7, and 9. Adenine and guanine maintain this basic structure but have characteristic substituents. Adenine has an amino group attached to Carbon 6. However, Guanine has an amino attached to Carbon 2 and a carbonyl at Carbon 6.

purines capable of watson-crick base pairs

For this element of their model, Watson and Crick had a key hint in the form of Erwin Chargaff’s recent finding that the sum of purines (Adenine and Guanine) always equaled the sum of pyrimidines (Thymine and Cytosine) in any stretch of DNA. From this, Watson and Crick found that both purines had a corresponding pyrimidine with which it “fits” together.

Watson-Crick Base Pair: Adenine and Thymine

Watson and Crick observed that adenine and thymine had two pairs of chemical groups capable of forming hydrogen bonds simultaneously:

The amino of the adenine and the carbonyl of the cytosine
The unsaturated nitrogen in the six-membered ring of adenine and the saturated nitrogen in the ring of thymine

Watson-Crick Base Pair: Guanine and Cytosine

Watson and Crick observed that guanine and cytosine had three pairs of chemical groups capable of forming hydrogen bonds simultaneously:

The carbonyl of the guanine and the amino of the cytosine
The saturated nitrogen in the six-membered ring of guanine and the unsaturated nitrogen in the ring of cytosine
The amino of the guanine and the carbonyl of the cytosine

guanine and cytosine watson-crick base pair

Additionally, since the guanine-cytosine pair involves one additional hydrogen bond than the adenine-thymine pair, DNA strands have a stronger affinity to one another with higher guanine-cytosine pairs or higher “GC” content. Higher GC content, in turn, increases the “melting” or “denaturing” temperature required to separate the DNA strands spontaneously. This has important implications for certain molecular biology lab techniques, such as PCR, which depend on DNA strands separating at specific temperatures.

Non-Watson-Crick Base Pairs

Although DNA, and RNA as well, tend to involve Watson-Crick base pairs exclusively, there exist more “non-canonical” base pairs. These alternate base pairs can be found in DNA under acidic conditions or certain RNA structures.

Hoogsteen Base Pairs

In Hoogsteen base pairing, guanine still pairs with cytosine and adenine still pairs with thymine. However, the pyrimidine bases, guanine and adenine, “flip” 180° relative to their Watson-Crick orientation. Biochemists call this “flipped” orientation the syn confirmation, as opposed to the anti orientation in Watson-Crick base pairing.

Between adenine and thymine, two hydrogen bonds still form between the following pairs of groups:

The amino group of adenine and the carbonyl of thymine
The unsaturated nitrogen in the five-membered ring of adenine and the saturated nitrogen in the ring of thymine

Between guanine and cytosine, two hydrogen bonds (instead of 3) form between the following pairs of groups:

The carbonyl of guanine and the amino of cytosine
The unsaturated nitrogen in the five-membered ring of guanine and the protonated nitrogen in the ring of thymine

differences between hoogsteen and watson-crick base pairs

Notice: in the guanine-cytosine pair, the ring nitrogen of cytosine must be protonated to form the necessary hydrogen bond. Because of this, Hoogsteen base pairing tends to be favored in low pHs, while Watson-Crick base pairing predominates at neutral or high pHs.

Interestingly, since the usual bonding groups of adenine and guanine remain unpaired, triplex DNA is possible through Hoogsteen base pairing. However, these structures tend not to form under most conditions.

Wobble Base Pairs

In transcription, RNA polymerases rely on Watson-Crick base pairing to determine the code of mRNA strands. In translation, however, what biochemists call “wobble” base pairs also exist in the interaction between mRNA and tRNA.
Intriguingly, tRNA has an alternate pyrimidine base called hypoxanthine, which forms the nucleotide inosine.

hypoxanthine, a pyrimidine capable of bonding with multiple other nitrogenous bases — Hypoxanthine, the nitrogenous base that corresponds to the nucleotide inosine.

Hypoxanthine resembles guanine, minus the amino group. Functionally, hypoxanthine forms two hydrogen bonds in base pairs with uracil, cytosine, and adenine. These hydrogen bonds form specifically from hypoxanthine’s carbonyl and saturated nitrogen.

Aside from these three new base pairs with hypoxanthine, guanine can also form a wobble base pair with uracil. Both hydrogen bonds form between their carbonyls and saturated nitrogens.

These alternate non-Watson-Crick base pairs allow for the redundancy of the genetic code. When placed in the third position of the tRNA anticodon, uracil, guanine, and hypoxanthine can bond with multiple possible mRNA bases.

For instance, the aminoacyl-tRNA with an anticodon of UAI always has an isoleucine amino acid. Due to the wobble base pairing of hypoxanthine, the mRNA codons of AUC, AUA, and AUU all bond to it, and thus all code for isoleucine in the final protein.