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Secrets of a precision protein machine
Date:4/15/2011

"pseudo-DNA" to whose backbone the polymerase can start adding DNA nucleotides to match with the template. The polymerase keeps on adding nucleotides until it runs into the RNA primer from the previous start.

This doesn't happen often on the so-called leading strand of the unwound DNA, where the polymerase usually proceeds smoothly, as if on a one-way street. The one-way direction, named for the chemical composition of the nucleotides at opposite ends of a DNA strand, is 5' to 3' (five-prime to three-prime).

On the lagging strand, however, the one-way street runs in the opposite direction, so replication has to be done in many little discrete fragments assembled "backwards," each started by an RNA primer. Called Okazaki fragments, these are only about 100 nucleotides long in humans, and some 50 million of them are added to the lagging strand during a human cell's replication.

When polymerase runs into the RNA primer of a previous fragment it peels it away like a chisel, leaving a long tail or "flap" of excess single-strand DNA at the 5' end. This flap must be clipped off before the new fragment can be joined failure to do this accurately would leave a gap or overlap that could cause a genetic mutation or rearrangement resulting in damaged chromosomes. FEN1 cuts off the flap and precisely prepares it for joining to the newer fragment, which is also left with a tiny flap, known as the 3' overhang.

Just how does FEN1 do the job? Tainer notes that many important structural features of human FEN1 were known from studies in 2007 by Shigeru Sakurai of Japan's Nara Institute of Science and Technology and from work on related FEN from microorganisms known as archaea. These studies were done without FEN1 acting on DNA, however, and many questions remained.

For example, FEN1 was long thought to move into position by sliding down the 5' flap to the incision site, like a bead on a string. The 5' flap passes through an opening
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Contact: Paul Preuss
paul_preuss@lbl.gov
510-486-6249
DOE/Lawrence Berkeley National Laboratory
Source:Eurekalert  

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