That perfect reproducibility strongly suggested to Bustamante and his colleagues that they were seeing a condensed structure with a well defined organization. Every time we pulled it out and relaxed it, the molecule was able to return to the same initial or condensed form, said Bustamante. In fact, the researchers pulled and relaxed the same DNA molecule dozens of times, seeing the same sawtooth pattern of extension and condensation each time.

They also found that the energy-containing ATP molecule appeared to play a regulatory role, rather than providing energy for the condensation reaction. When the researchers removed all excess ATP from the solution, they found that the condensin proteins continued to function. That finding was a big surprise, because we expected the protein to be more like a motor that had to burn ATP every time it condensed, said Bustamante. Also, when they removed the excess protein from the solution, the bound protein was able to recondense the DNA when the tension on the DNA was lowered.

The researchers' analyses led them to propose a model of how the string of condensin proteins interacts to condense the DNA molecule. They theorize that the heads of the condensin proteins attach themselves sequentially and tightly to DNA. By attaching in this fashion, each protein cooperates with its neighbor, binding itself reversibly to the head of the next protein, thereby scrunching the DNA bit by bit into its condensed state. And when the researchers experimentally stretched the DNA molecule, the condensin heads popped apart sequentially, producing the sawtooth force extension pattern. But the heads remained bound to the DNA, so that when the force is lowered they can go back to their closed state and recondense the DNA molecule.

According to Bustamante, these studies of the bacterial condensin molecule will open the way to future studies of similar proteins that manipulate DNA and maintain chromosomal structure. The actual mechanism by which these molecules actually carry out their function is unknown, he said. And so, we are very excited that we have been able to develop an assay that, for the first time, gives us an understanding of how these molecules may be acting at the molecular level.

hhmi