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October 09, 2010

DNA springs mechanically control the reaction of an enzyme

UCLA researchers attached a controllable molecular spring made of DNA to the enzyme. The spring is about 10,000 times smaller than the diameter of a human hair. They can mechanically turn the enzyme on and off and control how fast the chemical reaction occurs. In their newest research, they attached the molecular spring at three different locations on the enzyme and were able to mechanically influence different specific steps of the reaction.

(H/T Foresight Institute)


"We have stressed the enzyme in different ways," Zocchi said. "We can measure the effect on the chemical reaction of stressing the molecule this way or that way. Stressing the molecule in different locations produces different responses. If you attach the molecular spring in one place, nothing much happens to the chemical reaction, but you attach it to a different place and you affect one step in the chemical reaction. Then you attach it to a third place and affect another step in this chemical reaction."

Zocchi, Tseng and Wang studied the rate of the chemical reactions and reported in detail what happened to the steps of the reactions as they applied mechanical stress to the enzyme at different places.

"Standing on the shoulders of 50 years of structural studies of proteins, we looked beyond the structural description at the dynamics, specifically the question of what forces — and applied where — have what effect on the reaction rates," Zocchi said.

In a related second paper, Zocchi and his colleagues reached a surprising conclusion in solving a longstanding physics puzzle.

When one bends a straight tree branch or a straight rod by compressing it longitudinally, the branch or rod at first remains straight and does not bend until a certain critical force is exceeded. At the critical force, it does not bend a little — it suddenly buckles and bends a lot.

"This phenomenon is well known to any child who has made bows from hazelnut bush branches, for example, which are typically quite straight. To string the bow, you have to press down on it hard to buckle it, but once it is bent, you need only a smaller force to keep it so," Zocchi said.

The UCLA physicists studied the elastic energy of their DNA molecular spring when it is sharply bent.

"Such a short double-stranded DNA molecule is somewhat similar to a rod, but the elasticity of DNA at this scale was not known," Zocchi said. "What is the force the DNA molecular spring is exerting on the enzyme? We have answered this question.

"We find there is a similar bifurcation with this DNA molecule. It goes from being bent smoothly to having a kink. When we bend this molecule, there is a critical force where there is a qualitative difference. The molecule is like the tree branch and the rod in this respect. If you're just a little below the threshold, the system has one kind of behavior; if you're just a little above the threshold force, the behavior is totally different. The achievement was to measure directly the elastic energy of this stressed molecule, and from the elastic energy characterize the kink."


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