August 7, 2007

C.U. Researchers Discover How DNA Strands Separate

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The mystery of how DNA unravels has been unraveled by a team of Cornell researchers.
The culprit responsible for this important reaction, which enables the two-stranded DNA molecule to “unzip” and make copies of itself to be deposited into new cells, is an enzyme called helicase. It has long been known that helicases play an important role in separating the double helix of DNA, and that it moves incrementally along one of the DNA strands like a zipper-pull. Until recently, however, it had been unclear whether helicases actively force the helix open or passively wait for it to unwind on its own.
Now it looks like this debate may be resolved in favor of the active mechanism. A group of biophysicists from Cornell and Robert Wood Johnson Medical School in New Jersey published a paper in the most recent issue of the journal Cell, in which they describe how these “molecular motors” work.
According to Daniel Johnson grad, the lead author of the paper, scientists had originally imagined helicase as being either an opportunist or a go-getter. The opportunist helicase simply waits for its moment to arise.
“The fork junction [or the place where two partially-unraveled strands of DNA meet] can fluctuate open and closed due to thermal energy,” said Johnson. “There’s some probability that it will be open at any time, though that probability is very low. You can imagine that at some point the fork fluctuates open, and then the helicase steps forward. It doesn’t actually do anything to get the DNA to unwind; it just waits for the right moment.”
The go-getter helicase is more aggressive: it actually exerts a force on the fork junction to push the strands of DNA apart and force them to unwind. According to Johnson and his colleagues’ research, it looks like the aggressive helicase wins out. “A simple passive unwinding mechanism does not explain our data,” said Prof. Michelle Wang, physics, the senior author of the paper.
The team came to this conclusion after a number of experiments. They measured how fast helicase moves along a single strand of DNA. This is the fastest rate possible for helicase, because it doesn’t have to slow down to unwind the helix. They also directly measured how quickly helicase unwinds the helix. Finally, they unzipped DNA mechanically by anchoring the end of one strand to a surface and attaching a bead to the other strand, then sliding the bead along the strand to force the helix open. This allowed them to measure the force at the fork junction. They compared the rates they measured with theoretical models of how fast helicase would move if it were active or passive.
“By looking at the relationship between how fast helicase can move and the force, we can figure out how it moves — whether it interacts with the fork junction, or whether it waits for the fork junction to open and then moves forward,” Wang said.
“We found that the rate that the helicase moves is too fast to be explained by a passive unwinding model,” Johnson said. “It looks like the helicase actually does something to the fork junction to make it more likely that it will be open.”
This result will provide scientists with a better fundamental understanding of the nature of DNA replication, or how DNA is copied and implanted into new cells, which in turn will give them a better understanding of our evolutionary history.
“DNA replication is very important,” Wang said. “We all started as a single cell, but eventually we became multi-cellular, complicated organisms. For that, we needed helicase.”
This research may also have important implications for medical science.
“In order to replicate DNA, repair DNA, or splice chromosomes, you need helicase,” Johnson said. “It’s absolutely critical to cellular life.”