The Structure of DNA

- August 07, 2019

The Structure of DNA

Do you recognize this molecule?

This is DNA, or deoxyribonucleic acid.

By the end of this blog, you will be able to identify the key structural features of DNA, as well as describe the importance of those features for function.

We will look at different representations of the DNA molecule to better view certain details, but all views represent this same structure.

Inside the cell, you will most commonly find double- stranded DNA, in which two strands intertwine

to form a double helix. The most common form of the DNA double helix, which is what we will discuss here, is also called B-form DNA.

Now, let's move to a more simplified representation of DNA to discuss the details. We can unwind the double helix like this so that we can see the chemical structure inside.

Each strand is a polynucleotide, meaning the strand is made up of many individual units called nucleotides.

A nucleotide has three components, the five carbon sugar, a phosphate group, and one of four possible nitrogenous bases-- adenine, guanine, thymine, and cytosine.

Adenine

Guanine

Thymine

Cytosine

The nitrogenous base is always attached at the one prime carbon of the sugar. If we count from there, we can see that there is a phosphate between the five prime carbon of one sugar and the three prime carbon of the neighboring sugar.

The sugar is called deoxyribose because it is missing a hydroxyl group at the two prime carbon, which is present in ribose.

Because of this, nucleotides in DNA, deoxyribonucleic acid, are called deoxynucleotides.

Nucleotides attach to each other in the DNA strand by phosphodiester bonds. The phosphate group of one nucleotide binds to the three prime oxygen of the neighboring nucleotide. Thus, we can see that the sugars and phosphate groups make up the DNA backbone. The carbon numbering is key to describing the directionality of the DNA strand, five prime to three prime.

Phosphodiester bond

Looking within the sugars, there is an intrinsic orientation difference between the two strands. On the top strand, you can see that the five prime carbon of each sugar is on the left and the three prime carbon is on the right. The opposite is true for the bottom strand. Reading left to right, that makes the top strand orientation five prime to three prime and the bottom strand orientation three prime to five prime. These strands are also sometimes called Watson and Crick.

Keep in mind that this double- stranded DNA is still a double helix and we have simplified the representation by flattening and unwinding the helix here to better see the atomic structure.

Although the nucleotides come together through covalent bonds in the backbone, the two DNA strands interact through non-covalent hydrogen bonds between the bases. Each base forms multiple hydrogen bonds with its complementary base on the opposite strand. Bound together by hydrogen bonds, each unit is called a base pair.

The hydrogen bonding contributes to the specificity of base pairing. Thymine preferentially pairs with adenine through two hydrogen bonds and cytosine preferentially pairs with guanine through three hydrogen bonds.

Thymine and cytosine are called pyrimidines, characterized by their single ring structure, and adenine and guanine are called purines, which have double rings.

The geometry of the AT or TA and GC or CG base pairs is the same, allowing for symmetry and base stacking in the helix. This mostly has to do with the distance between the backbones and the angles to which the bases attach to the backbone. Other base pairs, like GT, for example, do not have the same geometry, cannot form strong hydrogen bonds, and disturb the helix.

The double helix structure of DNA is highly regular. Each turn of the helix measures approximately ten base pairs.

In addition to the hydrogen bonding between the bases, the stacking of the bases also stabilizes the double helix structure. These pi-pi interactions form when the aromatic rings of the bases stack next to each other and share electron probabilities.

The regularity of the helical structure forms two repeating and alternating spaces, called the major and minor grooves. These grooves act as base pair recognition and binding sites for proteins. The major groove contains base pair specific information while the minor groove is largely base pair nonspecific. This is because of the patterns of hydrogen bond acceptors and donors that proteins can interact with in the grooves.

In this way, the DNA can be acted upon in either a sequence specific or non-sequence specific manner, allowing proteins to position themselves correctly in the genome to carry out their designated tasks.