How DNA is formed

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Everyone's heard of DNA before - it's that thing inside us which defines us genetically. At least, that's the extremely generic concept. 

DNA is a polymer that consists of three key components:

  • a nucleobase, which is a compound that includes nitrogen;
  • this is then bonded to a sugar known as a deoxyribose;
  • and each of these molecules is connected with a phosphate group, forming a nucleotide which can bond with other nucleotides as a polymer.

This is the basic structure of DNA.

Photo 51 - image taken of DNA, in 1952. Note the double helix.

Nucleobases

How I've described nucleobases sounds extremely vague. You could argue ammonia could be a nucleobase, after all it has nitrogen. But when it comes to DNA, there's are specific types of nucleobase which are allowed.

Purine (left) and pyrimidine (right). Purine is simply a pyrimidine and imidazole fused together!

Nucleobases consist of flat, aromatic rings, often based on a purine or a pyrimidine structure. In DNA, there are four different types of nucleobase which exist (from now on, I'll refer to them by their shorthand letter form):

  • adenine (A)
  • cytosine (C)
  • guanine (G)
  • thymine (T)

A and G are based on purine, C and T are based on pyrimidine.

These nucleobases consist of hydrogen bond acceptors (which consist of oxygens or nitrogens with lone pairs) and donors (such as hydrogens), which will be important in a moment, as these will enable the building of the double-helix structure that DNA is known for.

Ribose

Ribose is a sugar, general formula C5H10O5; specifically. β-D-ribofuranose, which is a specific stereoisomer of ribose:

Ribose 

This will be important later on, when I get onto RNA. But for now, let's lose the OH bonded to the carbon at the 2' position:
 

Deoxyribose

We've deoxygenated the sugar, so we're left with a deoxyribose. The hydroxy group was lost at 2', so it's 2'-deoxyribose. This is the form of deoxyribose that features in DNA. 

Now you might assume we'll form bonds at 2', but we don't. At 1', the hydroxy group will be substituted for a nucleobase, and at 3' and 5', we'll lose the hydrogen in the hydroxy group and substitute it for a phosphate. If we bond the nucleotides together, we will form a phosphodiester bond between them, and if you continue doing this, you'll eventually end up with a polynucleotide. We're halfway there.

Building the double-helix

DNA consists of a double helix structure, where two polynucleotides are bonded anti-parallel to each other. You can have hydrogen bonds between different nucleotides, for instance, under very simple conditions:

  • When you have an A nucleobase, it can only form hydrogen bonds with a T nucleobase, and vice versa;
  • The same applies with C and G.

This is because A/T and C/G are complementary to each other in terms of shape and structure; A and T can form two hydrogen bonds with each other, C and G can form three. This on the whole maximises stability. Notably, if you have a C-G base pair, it will be complementary in size to a T-A base pair, and vice versa. 

When you combine these polynucleotides in this way, you'll end up with a double helix, consisting of a major and minor groove which repeats as you move up the structure. The nucleobases are non-polar and tightly packed, repelling water and maximising stability on the inside. Meanwhile, the phosphate groups on the outside are negatively charged - this is favourable to water, which is polar, and forms an electrostatic attraction between water and the phosphates. The balance between the hydrophobic core and hydrophilic exterior ultimately makes DNA very soluble and hydrophilic in the end, since the attraction with water far outweighs the nucleobase's hydrophobic effects, whilst still maximising stability.

What about RNA?

RNA is very similar to DNA except this time:

  • it consists of only one strand;
  • consists of a ribose sugar, as seen earlier (hence the name ribonucleic acid);
  • instead of thymine (T), you have uracil (U), which acts in much the same way - A generally forms hydrogen bonds with U, and vice versa. But not all the time.
Uracil. It's not that different to thymine, all you've done is remove a methyl group!

Numbering

Worth noting that when you combine nucleobases in RNA or DNA to form a nucleic acid, the actual structure is written depending on the direction that the nucleic acid is moving in. Generally, it's written from the 5' to the 3' direction, like this:

And in DNA, when you have the antiparallel strands, one will be moving in the 5' to 3' direction, and the other will move from 3' to 5'. 

But more on that in my inevitable blogpost on protein synthesis. 

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