Saturday, August 25, 2007

a short DNA primer for the future: sticky ends

This is probably the first of a series of my personal tutorials on building stuff with DNA. I am sure as things get more complicated I will cop out and just link to some fine resources, but for now you're getting my take on things. This may be review for some, but not for others, and I would like to build a one-stop-shop for the information I may use in the future. I did do a couple science fair projects involving DNA in junior high. One included building a model out of dowel rod and window blinds. It rotated. I got an A++ (brag!). The other was an ill fated attempt to mutate Oak trees which I may still revisit one day. Unfortunately due to time constraints, I must assume you did a couple similar projects in school too, so you would know all the DNA- "blue print of life" stuff. Please let me know of any errors.

Let's just dive in...

For building DNA structures we first need to focus on the structure of DNA itself and how strands of DNA join (or won't join) together.

The frame work, or backbone, of a DNA strand is composed of alternating sugar and phosphate groups. I am going to represent these by S and P respectively.

So we have a chain of:

These sugars are the deoxyribose in deoxyribose nucleic acid, and they come in two kinds: 3' and 5' (pronounced 3-prime and 5-prime). The 3 and the 5 represent how many carbon atoms the sugar contains.

A single strand of DNA will have alternating sugar groups and alternating ends:

But doesn't most DNA come double stranded?
YES, so the groups on a double strand of DNA would look like this:

These strands are connected together by hydrogen bonding of the nucleotides, A, T, C, G

I have developed a somewhat "blue" method for remembering which nucleotides join up. I was inspired by a pin-up art calendar a friend bought me for Christmas years ago: Just remember T and A always go together.

The nucleotides join up at the sugars:
A---T--- C---G
The dashes between nucleotides are just for formatting purposes

Also it is probably important to point out that hydrogen bonds are weak bonds, allowing the DNA to seperate.

If we have a strand of DNA, it is possible to cut it apart using an enzyme called a restriciton endonuclease. These enzymes can cut apart a strand of DNA in a manner that leaves a "sticky end", meaning an end that would happily join to a sticky end of another DNA strand:



Here the overhanging nucleotides form the sticky end. I used NE1 to create sticky ends on the DNA chains in the cross structure I built last night.

So that was the first DNA tutorial.


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