DNA Structure

DNA is what life is built on. Each of our cells has DNA strands that measure 6 feet long in total if you’d uncoil them all. How do these strands fit into a 0.0002 inches long cell¹? Well, DNA structure allows it to organize in such a way that makes this possible!

Fig. 1: You're probably familiarized with the double helix structure of DNA. However, this is only one of the levels in which DNA structure is organized.

• Here, we are going to run through the structure of DNA.
• First, we’ll focus on DNA nucleotide structure and complementary base pairing.
• Then, we’ll move up to the molecular structure of DNA.
• We’ll also describe how the structure of DNA is related to its function, including how a gene can code for proteins.
• In the end, we will discuss the history behind the discovery of DNA structure.

DNA Structure: Overview

DNA stands for deoxyribonucleic acid, and it is a polymer composed of many small monomer units called nucleotides. This polymer is made from two strands that are wrapped around each other in a twisting shape that we call a double helix (Fig. 1). To understand the DNA structure better, let's take just one of the strands and then untwist it, you'll note how the nucleotides form a chain.

Fig. 2: A single strand of DNA is a polymer, a long chain of smaller units called nucleotides.

DNA Nucleotide Structure

As you can see in the diagram below, each DNA nucleotide structure consists of three different parts. On one side, we've got a negatively charged phosphate which is connected to a closed deoxyribose molecule (a 5-carbon sugar) which is itself bonded to a nitrogenous base.

Fig. 3: The structure of DNA nucleotides: a deoxyribose sugar, a nitrogenous base, and a phosphate group.

Every nucleotide has the same phosphate and sugar groups. But when it comes to the nitrogenous base, there are four different types, namely Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). These four bases can be classified into two groups based on their structure.

• A and G have two rings and are called purines,
• while C and T only have one ring and are called pyrimidines.

Since each nucleotide contains a nitrogenous base, there are effectively four different nucleotides in DNA, one type for each of the four different bases!

As we mentioned before, the DNA molecule is composed of two polynucleotide strands. These two strands are held together by hydrogen bonds formed between pyrimidine and purine nitrogenous bases on opposite strands. Importantly, though, only complementary bases can pair with each other. So, A always has to pair with T, and C always has to pair with G. We call this concept complementary base pairing, and it allows us to figure out what the complementary sequence of a strand will be.

Since A always pairs with T, and G always pairs with C, the proportion of A nucleotides in the DNA double helix is equal to that of T. And similarly, for C and G, their proportion in a DNA molecule is always equal to each other. Furthermore, there are always equal amounts of purine and pyrimidine bases in a DNA molecule. In other words, [A] + [G] = [T] + [C].

Hydrogen bonds between DNA nucleotides

Certain hydrogen atoms on one base can act as a hydrogen bond donor and form a relatively weak bond with a hydrogen bond acceptor (specific oxygen or nitrogen atoms) on another base. A and T have one donor and one acceptor each hence they form two hydrogen bonds between each other. On the other hand, C has one donor, and two acceptors and G has one acceptor and two donors. Therefore, C and G can form three hydrogen bonds between each other.

Molecular Structure of DNA

Now that we learned the structures of DNA nucleotides, we'll see how these form the molecular structure of DNA. If you had noticed, the DNA sequences in the last section had two numbers on either side of them: 5 and 3. You may be wondering what they mean. Well, as we said, the DNA molecule is a double helix composed of two strands that are paired together by hydrogen bonds formed between complementary bases. And we said that the DNA strands have a sugar-phosphate backbone that holds the nucleotides together.

Fig. 4: The molecular structure of DNA consists of two strands forming a double helix.

Now, if we look closely at a DNA strand, we can see that the two ends of a sugar-phosphate backbone are not the same. At one end, you have the ribose sugar as the last group, while at the other end, the last group must be a phosphate group. We take the ribose sugar group as the beginning of the strand and mark it with 5'. by scientific convention And you must have guessed it, the other end that finishes with a phosphate group is marked with 3'. Now, if you are wondering why that is important, well, the two complementary strands in a DNA double helix are, in fact, in the opposite direction of each other. This means that if one strand is running 5' to 3', the other strand would be 3' to 5'!

So if we use the DNA sequence that we used in the last paragraph, the two strands would look like this:

5' TCAGTGCAA 3'

3' AGTCACGTT 5'

The DNA molecule is very long, therefore, it needs to be highly condensed to be able to fit inside a cell. The complex of a DNA molecule and packaging proteins called histones is called a chromosome.

DNA Structure and Function

Like everything in biology, DNA structure and function are tightly related. The characteristics of the DNA molecule structure are tailored for its main function, which is to direct protein synthesis, the key molecules in the cells. They perform various essential functions such as catalysing biological reactions as enzymes, providing structural support for cells and tissues, acting as signalling agents, and many more!

Fig. 5: DNA structure and function: the sequence of nucleotides in the DNA codes for the sequence of aminoacids in a protein.

The genetic code

You might have already heard of the term genetic code. It refers to the sequence of bases that code for an amino acid. Amino acids are the building blocks of proteins. As mentioned earlier, proteins are a huge family of biomolecules that do most of the work in living organisms. Cells need to be able to synthesise a plethora of proteins to perform their functions. The DNA sequence, or more specifically the DNA sequence in a gene, dictates the sequence of amino acids for making proteins.

In order to do this, each group of three bases (called a triplet or a codon) codes for a specific amino acid. For example, AGT would code for one amino acid (called Serine) while GCT (called Alanine) codes for a different one!

DNA self-replication

Now that we have established that the sequence of bases in the DNA determines the sequence of amino acids in proteins, we can understand why it is important for the DNA sequence to be passed on from one generation of cells to another.

The complementary base pairing of nucleotides in the DNA structure allows the molecule to replicate itself during cell division. During the preparation for cell division, the DNA helix separates along the centre into two single strands. These single strands act as templates for the construction of two new double-stranded DNA molecules, each of which is a copy of the original DNA molecule!

The Discovery of DNA Structure

Let us dive into the history behind this big discovery. American scientist James Watson and British physicist Francis Crick developed their iconic model of the DNA double helix in the early 1950s. Rosalind Franklin, a British scientist, working in the lab of physicist Maurice Wilkins, provided some of the most important hints regarding the structure of DNA.

Franklin was a master in X-ray crystallography, a powerful technique for discovering the structure of molecules. When an X-ray beams strike the crystallized form of a molecule, such as DNA, part of the rays are deflected by the atoms in the crystal, generating a diffraction pattern that reveals information about the molecule's structure. Franklin's crystallography provided vital hints to Watson and Crick on the structure of DNA.

Franklin and her graduate student's renowned "Photo 51", a highly clear X-ray diffraction picture of DNA, provided vital clues to Watson and Crick. The X-shaped diffraction pattern instantly indicated a helical, two-stranded structure for DNA. Watson and Crick assembled data from a variety of researchers that, included Franklin and other scientists, to create their famous 3D model of the DNA structure.

Fig. 6: X-ray diffraction pattern of DNA.