To their surprise, the scientists observed how the enzyme, DNA polymerase, retains a "short-term memory" of mismatches, in some cases halting itself past the point of the mismatch, so that the repair machinery can go to work. They also found that the mismatch structures differed dramatically from those deduced from previous indirect biochemical studies.
In an article in the March 19, 2004, issue of the journal Cell, Duke University Medical Center biochemists Sean Johnson and Lorena Beese, Ph.D., described how they had conducted detailed structural analyses of DNA polymerase as it encountered each of the 12 possible kinds of mismatches possible in DNA replication.
In such replication, the polymerase sequentially attaches DNA units called bases along a single-stranded template DNA. The result is like constructing one rail of a spiral staircase, using the other rail as a guide; and the polymerase "translocates" the template strand through its active site like a thread through the eye of a needle.
In this replication process, the polymerase normally guides the template strand and assembles the complementary, growing "primer" strand by pairing each base with the correct counterpart -- always pairing adenine with thymine and cytosine with guanine.
When mismatches occur, the polymerase must instantly halt itself, triggering the mismatch repair machinery to launch into action, before replication can continue. This stalling is thought to occur because the polymerase-DNA structure is distorted by the mismatched bases, causing it to shut down.