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Silencing a Gene: It’s a Stretch

Photonics.com
Mar 2011
TUCSON, Ariz., March 23, 2011 — Cells may control genes simply by stretching them, a discovery that could pave the way for applications that require precise control over gene expression, such as lab-on-a-chip devices.

For living organisms to function properly, the activity of genes contained within the DNA must be precisely regulated. To activate a gene and read out its information, a cell must activate certain components of its biochemical machinery.


Playing tug-of-war with DNA: This illustration shows the experimental setup: Laser beams (red cones) trap two beads connected by a strand of DNA. The researchers then slowly lower the beads until the DNA gets close enough for an RNA polymerase enzyme (blue) to latch on. (Image: Gary Skinner)

First, an enzyme called RNA polymerase must latch onto a specific binding site on the DNA and unwind the two strands that make up the double helix. The enzyme then travels along the stretch of DNA, reading out the information and making a copy in the form of an RNA molecule. 

Along with his colleages, Koen Visscher from the College of Optical Sciences and the University of Arizona's BIO5 Institute took advantage of optical tweezers to manipulate and move around the molecular players as required for the process of gene activation to study how they interact. 

At the heart of the optical tweezers' apparatus is an infrared laser capable of trapping tiny particles and holding them in place. Researchers attach a single DNA molecule to plastic beads so small that tens of them in a row would barely reach across a human hair.

“We trap one of those beads in our optical tweezers,” Visscher said. “Then we go in with a second trapped bead carrying an antibody capable of attaching to the DNA and run it into the first bead. The idea is to try and catch the loose end of the DNA. It’s like fishing for DNA.”

This fishing expedition can take a long time. Because the DNA is too small to see even with a microscope, the researchers use the optical tweezers to slightly tug on one bead and watch whether the other moves in response.

“If it does, we know we hooked the DNA,” he said.

Once both beads connected by the strand of DNA are trapped, the scientists make one of the beads oscillate back and forth. The DNA transmits the movement, causing the bead on the other end to oscillate as well.


Koen Visscher, associate professor in the University of Arizona's department of physics, adjusts the microscope attached to the optical tweezers setup. Visible in the foreground is part of the laser apparatus used to hold the beads in place. (Image: Patrick McArdle/UANews)

To measure the interaction between the DNA and the RNA polymerase molecule, a third bead comes into play: Studded with a few RNA polymerase molecules and attached to a microscope slide, it is placed underneath the outstretched DNA molecule, which contains an RNA polymerase binding site, a specific code sequence that the enzyme recognizes and binds to.

“We slowly lower the DNA onto the enzyme,” said Visscher. “Once it latches onto the DNA, it inhibits the transduction of force between the beads. It’s like two children pulling back and forth on an elastic band until a frustrated parent grabs it in the middle and puts an end to the horseplay. In our case, the RNA polymerase has the same effect: The DNA strand can no longer transmit the oscillations from the first bead to the second, causing it to stop moving. That is how we know if the polymerase has bound to the DNA.”

The discovery came when the researchers pulled on the two beads holding the DNA, gradually increasing the tension. At some point, the gene was no longer read.

“As we increase the tension, we see that the enzyme finds it harder and harder to latch on,” he said, “to the point where it still binds but falls off almost immediately.”

The force applied to the DNA strand ranges from 1 piconewton to 12 piconewton, about 50,000 times weaker than the weight of a grain of salt.

“If we apply too much force, we alter the structure of the DNA. If we change the structure of the DNA, all bets are off as far as the interaction with the protein goes. We want to be far away from that,” Visscher said. “There are a lot of ways to biochemically control the activity of genes on those chips, but we believe there is another way – you can do it by force. Picture a chip with DNA molecules attached to it. If you attach a magnetic bead to the end of certain DNAs and place an electromagnet above that chip, you could switch certain genes on or off, simply by stretching or relaxing the DNA.”

What about nature? Is it possible that organisms use DNA stretching as a way to control their gene expression?

“We don’t know that yet for sure,” Visscher said. “But if one looks at how DNA is packed in a cell’s nucleus, one finds that there is a lot of stretching and twisting going on, so it’s possible.”

For more information, visit:  www.arizona.edu 


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