Scientists have gotten a close look at a process that is fundamental to life on earth - DNA replication. Reporting in Cell, the researchers observed the replication of an individual molecule of DNA, and what they saw surprised them. There was a randomness to the process they did not expect.
"It's a different way of thinking about replication that raises new questions," said Stephen Kowalczykowski, Distinguished Professor in Microbiology and Molecular Genetics at the University of California, Davis.
During replication, the two strands that comprise the helix of DNA are unwound. Primers then move in to get the process started, and polymerase enzyme then begins the work of adding nucleotide bases to the new, growing strand of DNA. The two strands of DNA are a little different, however, because they run in opposite directions. As such, in one direction the polymerase moves along uninterrupted, while on the other the polymerase does not work continuously, and has to hop on and off of what is called the lagging strand.
It has been thought that there was some coordination of the replication, and one polymerase did not get that far ahead of the other. The results from this new work suggest that things actually work a little differently.
The investigators set up the replication in a flow chamber, and the DNA could tsretch out. They controlled the process by adding or removing fuel in the form of adenosine triphosphate, or ATP. A fluorescent dye that binds only to double-stranded DNA highlighted the new strands as they grew.
The investigators found that replication would unpredictably come to a halt, then start up again at a different speed. "The speed can vary about ten-fold," Kowalczykowski explained. They saw that the synthesis of the lagging strand might stop completely while the leading strand grew on, leaving a portion of single stranded DNA without dye attached.
"We've shown that there is no coordination between the strands. They are completely autonomous," Kowalczykowski noted. Random starts, stops and variable speeds were observed, although there was a similar average speed of replication overall, leading Kowalczykowski to use traffic on a freeway as an analogy. "Sometimes the traffic in the lane one over is moving faster and passing you, and then you pass it. But if you travel far enough you get to the same place at the same time.”
They also saw that a kind of automatic brake was working on the enzyme that unwinds the DNA strands at the start, called helicase. It actually slows down when the polymerase does, so that it keeps working while the other enzymes get back on track, and doesn’t leave unwound portions of DNA exposed during the. lag time.
The researchers feel this work will have a major impact. "It's a real paradigm shift, and undermines a great deal of what's in the textbooks," Kowalczykowski said.