Almost all life is based on DNA being copied or replicated. Now for the first time, scientists have been able to watch the replication of a single DNA molecule, with some surprising findings. For one thing, there is a lot more randomness at work than has been thought.
"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.
Using sophisticated imaging technology and a great deal of patience, the researchers were able to watch DNA from E. coli bacteria as it replicated and then measure how fast enzyme machinery worked on the different strands.
The DNA double helix is made from two strands that run in opposite directions. Each strand is made of a series of bases (A, T, C, and G) that pair up between the strands (A to T and C to G).
The first step in replication is an enzyme called helicase that unwinds and "unzips" the double helix into two single strands. An enzyme called primase attaches a "primer" to each strand that allows replication to start, and then another enzyme called DNA polymerase attaches at the primer and moves along the strand adding new "letters" to form a new double helix.
Because the two strands in the double helix run in opposite directions, the polymerases work differently on the two strands. On one strand (the "leading” strand) the polymerase can move continuously, leaving a trail of new double-stranded DNA behind it. But on the other strand (the "lagging” strand) the polymerase has to move in starts, attaching, producing a short stretch of double stranded DNA, then dropping off, and starting again. Conventional wisdom is that the polymerases on the leading and lagging strands are somehow coordinated so that one does not get ahead of the other.
Once the scientists started watching individual DNA strands, they noticed something unexpected. Replication stops unpredictably and, when it starts up again, can change speed. "The speed can vary about 10-fold," Kowalczykowski said. Sometimes the lagging strand synthesis stops, but the leading strand continues to grow. "We've shown that there is no coordination between the strands. They are completely autonomous."
What looks like coordination is actually the outcome of a random process of starting and stopping, plus variable speeds. Over time, any one strand will move at an average speed; look at a number of strands at the same time, and they will have the same average speed. Kowalczykowski likened it to traffic on a freeway. "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."