DNA Structure

DNA has a compact, highly organized structure that is reminiscent of a spiral staircase. There are several structural characteristics that are readily identifiable in DNA.

The DNA double-helix is formed by two right-handed, complementary strands of nucleotides coiled around each other. "Right-handed" is a term used to describe the symmetry of a 3-dimensional object. It means that if you place the thumb of your right hand along the long axis of the molecule and curl your fingers in, the chain "twists" in the same direction as your fingers.

The DNA double helix also has two different-sized "grooves": a major groove and a minor groove. These grooves are binding sites for a wide variety of molecules that affect DNA at the molecular level such as proteins that control such functions as gene expression, regulation, replication and transcription (to RNA). Additionally, other non-native molecules such as drugs, poisons, and carcinogens can bind to and affect DNA (see section 11.3 in your text-DNA damage and repair).

Although the overall structure of DNA seems fairly complicated, it is a polymer that is made up of four similar and simpler units. These simpler monomeric units are called nucleotides. They are:

The nucleotides in DNA are abbreviated as single letters, A for AMP, T for TMP, G for GMP and C for CMP. This makes the discussion of the order of bases in genes much easier.

Each nucleotide in turn is made up of 3 components, a phosphoric acid moiety, a pentose sugar - deoxyribose, and a "base" (technically, a heterocyclic amine) of which there are four kinds. There are two sub-types of bases, the bicyclic (double ring) purine bases, adenine and guanine; and the single ring, pyrimidine bases, thymine and cytosine.

The backbone structure of DNA is made up of alternating groups of phosphate and deoxyribose. The hydrophilic, polar backbone is in a position to directly interact with the aqueous environment of the cell.

Polymerization of the nucleotides to form nucleic acids involves linking the hydroxyl group on the 3 prime (3') carbon of deoxyribose of one nucleotide to the phosphate group of the next nucleotide. The phosphate is connected to the 5 prime (5') carbon on deoxyribose. The prime following a number denotes a carbon atom of the deoxyribose sugar, to distinguish them from the numbered carbons of the bases. This next movie shows the resulting 3',5'-phosphodiester bonds show (in 2D) in figure 10.7 of your textbook.

Repeating the simple step of linking two nucleotides together several thousands of times will yield a nucleic acid. This process is not at all random, and there is a high degree of order in DNA assembly-- or more correctly, DNA replication. The preservation of the order of the nucleotides in DNA is the key to inheritance of genetic characteristics. The replication process is mediated and regulated by a variety of enzymes as well as by the DNA itself. At the end of the replication process, a single "parent" double helix will generate two exact copies of itself.

In contrast to the hydrophilic backbone, the face of each base (as opposed to the edges) is hydrophobic and the bases are protected from interaction with water (darker blue atoms) by the structure of the double helix. This arrangement has a secondary purpose--it allows certain kinds of interactions that help stabilize the entire molecule (see below).

The starting and the ending points of the DNA chains are important to distinguish. The information contained in DNA only makes sense if it is read in the correct direction. This is true because DNA and RNA synthesis always goes from one specific end to the other, it is never read in both directions. The non-arbitrary starting point is the end of the chain that has an unlinked monophosphate. Since this group is connected to the 5th carbon in deoxyribose, we designate this as the 5' end. At the opposite end, the chain ends with an unlinked hydroxyl (OH) group at the number 3 carbon in deoxyribose. This terminus is designated the 3' end.

An interesting feature is that if we look at both strands in DNA we see that they run in opposite directions in terms of the 5' and 3' ends (see the difference between the purple and green strands). That is to say, the strands run antiparallel to each other. Thus, reading from the 5' to 3' end, the chain in the next movie would read C, G, G, and so on....

Commonly, we write this out in a highly condensed structural formula:
5'-CGGAGGACTGTCCTCCG-3'

The bases along the opposite strand of the double helix are in the following order:
3'-GCCTCCTGACAGGAGGC-5'
(Note that in formal contexts such as scientific literature we never write single-stranded nucleotide sequences in the 3' to 5' direction.)

Another way to determine the sequence of the opposite DNA strand is to know that G and C are always found directly opposite each other, as are A and T. Thus we write out the double-stranded DNA sequence as follows:

5'-CGGAGGACTGTCCTCCG-3'
3'-GCCTCCTGACAGGAGGC-5'

This matching up of A with T and G with C is called complementary base-pairing.

In the space filling model of DNA it may appear that the two chains are held together covalently. This however is not the case. The stability of the double helix can be attributed to two forces: hydrogen bonding between pairs of complementary bases (base pairing), and the van der waals forces between "stacked" bases (within each strand) due to interactions between the bases in an aqueous environment.

Hydrogen bonds: A base on one strand will form a specific number of hydrogen bonds with the base directly opposite it. The great number of these relatively "weak" attractive forces results in a strong net attraction between strands. In addition, due to functional group geometries of each base, only certain pairs of bases can exist. Pairing will always occur between a pyrimidine base and a purine base. Because of steric (crowding) and other factors, other combinations of these 4 bases are very unstable. This particular phenomenon is called base pairing.

Guanine and cytosine will always form a pair, sharing 3 hydrogen bonds.

Thymine and adenine will always form a pair, sharing 2 hydrogen bonds.

Base stacking: When ring structures such as those found in nucleotide bases are stacked flat against each other, they experience small forces of attraction. This is called base stacking, and though the individual forces are weak, like hydrogen bonds they become a major factor when you add them over several thousand base pairs. This structure shows the relative boundary of the atoms in each base as a dotted outline laying over the wirefame structure - notice the close proximity between the atoms of neighboring bases, and how the bases are stacked flat, one on top of each other.

In this tutorial so far we have discussed DNA in terms of a specific conformation example, B-DNA. This is the conformation that is the most commonly found under physiological conditions in a cell. It is also the conformation made famous by Watson and Crick in their Nobel Prize winning study to determine DNA structure. There are two additional forms of DNA commonly known, A-DNA and Z-DNA.

A-DNA is formed from B-DNA when it is chemically treated or is made anhydrous, and also forms under some biological conditions that are not yet well understood. This form of DNA is similar to B-DNA in several respects. They both have right-handed helices, antiparallel strands, and complementary base pairs. Major differences in the two structure are that A-DNA's length is more compact while it's diameter is greater than B-DNA.

Finally, Z-DNA is a form of DNA that has been found in both synthetic and short segments of native DNA. It is quite different then the previous two structures. First of all, it is a left-handed helix. It is also narrower than the other two types of DNA. Z-DNA also has a very unique zigzag arrangement of its covalent backbone.

To compare these three forms of DNA more closely, use the table below. Click on the name of the DNA form, and then change its display with the controls on the right.

Structure

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QUESTIONS

The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.

Question 1 - Load structure
What is the correct sequence of bases in the colored strand of the following A-DNA molecule?
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Question 2 - Load structure
How many base pairs are required to make a complete (360 degree) turn of this form of DNA?
View Answer


For specific instructions on how to manipulate the 3D images in this tutorial, see Structure Tutorial Help.


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