Tuesday, July 17, 2007
DNA Is a Polynucleotide
DNA is composed of nucleotides strung together to make a long chain called a polynucleotide. There are four basic nucleotides in DNA. They are; deoxyadenylate (A), deoxyguanylate (G), deoxycytidylate (C), and deoxythymidylate (thymidylate) (T).
There are a few things you need to know about the nucleotides in order to properly understand the structure of double-stranded DNA.
First, a nucleotide is composed of a base (adenine, guanine, cytosine, thymine) attached to a sugar (deoxyribose) to form a nucleoside. The nucleoside has an attached phosphate group and that makes it a nucleotide. The name of the nucleoside containing the base adenine is deoxyadenosine and if the phosphate group is attached at the carbon numbered 5′ (five prime) then the formal name of the nucleotide is 2′deoxyadenosine 5′-monophosphate (dAMP).
Those little numbers are important. The phosphate group can also be attached to the 3′ carbon to make another kind of nucleotide called 2′-deoxyadenosine 3′-monophosphate.
Normally the carbon atoms of the sugar are numbered 1, 2, 3 etc. but in a nucleoside the numbering of the nitrogen and carbon atoms of the base takes precedence. Thus, the sugar carbon atoms are numbered 1′, 2′ 3′ etc as shown on the left.
If you want to follow the discussion about DNA you have to take a bit of time right now and get familiar with the numbering of the sugar carbon atoms. Note that there's no attached hydroxyl group on the 2′ carbon atom. That's why this is 2′-deoxyribose.
You can string together a bunch of nucleotides to make single-stranded DNA. Inside the cell it's the job of DNA polymerase to make polynucletides from nucleotides. The structure of a typical polynucleotide (right) shows that the individual units are attached through their phosphate groups. The phosphate group on one 5′ carbon atom is attached to the 3′ carbon atom of the nucleotide above it.
This gives rise to the characteristic sugar-phosphate backbone of DNA. This linkage is called a 3′-5&prime (three prime, five prime) phosphodiester linkage. The bases are not involved in the covalent linkages between nucleotides.
This single-stranded polynucleotide chain has a free 5′ end at the top and a free 3′ end at the bottom and that's going to be true for all single-stranded chains. We're often interested in describing the directionality of this chain because it's important in synthesis and in degradation by nucleases. For example, the chain is synthesized in the 5′→3′ (five prime to 3 prime) direction. Which means that incoming nucleotides are added to the bottom of the chain during elongation.
By convention, the directionality is determined by reading across an individual nucleotide residue. In practice this means reading across a single deoxyribose sugar. Thus, reading from the top to the bottom of the strand shown above you cross the sugar carbons in the order 5′, 4′ and 3′. The direction is 5′→3′ (five prime to three prime). If you're talking about the direction from bottom to top then you read across the sugar in the order 3′, 4′, and 5&prime and the direction is 3′→5′ (three prime to five prime).