Thursday, June 17, 2010

My Research Explained: Stretching DNA

Things are happening in lab at an amazing rate now and I've decided to switch up the My Research Explained. In previous posts I've discussed how things work and how it relates to my research in particular, but I think it's time to fill you in on the cutting edge.

For the past couple of days, we've been getting some kind of result but until today it hasn't been proven. As you will see, we have conclusively stretched and overstretched DNA. While this result isn't groundbreaking in general it is for the lab and I'll explain why.
DNA is a double stranded polymer (as I've explained in the past). It is pretty stable in this form and it has to be to be able to withstand the environment of the body. It is strong enough to withstand forces from our optical tweezers and not break, but another interesting phenomenon occurs. Instead of snapping like a twig, DNA can stretch. 
We measure this stretching by measuring the position of the trap. Remember a long time ago I explained that the microspheres we use act like tiny lenses. So if the bead moves in the trap it refracts the light and changes it's position on our detector. When I'm doing my experiments I look at the output of the position of the trap and from this result I can more or less tell if I'm stretching DNA.
The video above shows what tethered microspheres look like. The beads are attached to a DNA strand and are constrained to the area that a DNA molecule can be extended to. If a bead isn't tethered it is free to diffuse in the solution. When we stretch DNA we grab a bead with our laser and move either the laser or the stage that the sample sits on. Since the bead is trapped by the light, when the laser moves the bead goes with it.

This is what DNA looks like to me when it is being stretched and overstretched.
This is a screenshot of our analysis software.
Look at the graph at the bottom of the image. That is a typical force vs extension curve. When the graph is approximately a flat line, the DNA is being stretched. When the line curves upward (indicating that higher forces are being exerted to continue stretching) the double-stranded DNA is basically at it's limit of stretching. Next the DNA undergoes some physical conformation where the bonds between the two strands are being broken so that the DNA can then be stretched again (overstretched) at a constant force.

This is very huge for the lab. We have been struggling for months trying to get the tweezers working properly and it seemed like we wouldn't be able to have enough force from the tweezers to unzip. The force required to overstretch DNA is much greater than the force required to unzip DNA and so getting this remarkable result means that we can definitely unzip DNA. Expect that result in the coming weeks!

Big things are ahead for the lab and for you all. I just can't wait to get there!

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