Researchers Unravel A Mystery About DNA

The discoveries, which inform our understanding of the structure and mechanics of RNAP -- an enzyme responsible for making RNA from a DNA or RNA template -- can help set the stage for new opportunities in combating bacterial diseases that kill 13 million people worldwide each year.

The researchers used single-molecule spectroscopy to monitor the transfer of energy between -- and hence the distance separating -- pairs of fluorescent chemical tags attached to key structural elements of RNAP and the DNA double helix during initiation of the transcription process.

The changes in the distances between these tags confirmed that transcription proceeds initially through a "scrunching" mechanism in which, much like a fisherman reeling in a catch, RNAP remains in a fixed position while it pulls the flexible DNA strand of the gene within itself and past the enzyme's reactive center to form the RNA product.

These changes are inconsistent with other theories that had suggested that RNAP moves along the DNA strand as a complete block in a process resembling the movement of an inchworm.

The research team is comprised of Achillefs N. Kapanidis, Emmanuel Margeat, Sam On Ho, Ekaterine Kortkhonjia and Shimon Weiss of the UCLA Department of Chemistry and Biochemistry, the Department of Physiology and the California NanoSystems Institute (CNSI). The team collaborated with Richard H. Ebright, Howard Hughes Medical Institute, Waksman Institute and Department of Chemistry, Rutgers University.

The scrunching model implies that the scrunched DNA is expelled from the enzyme channel at predictable sites that are available for interaction with transcription regulatory proteins. Beyond resolving the mechanism for initiation, the significance of this work is in pointing out an important regulation "checkpoint." Scrunched DNA is likely to play a major role in future studies of transcription regulation, and possibly become a focus for antibiotic drug discovery efforts.

"These are issues that we were not able to resolve until the development of the single molecule methods that we employed in these studies," Ebright said. "These methods involve detecting and manipulating single molecules, one at a time -- a breakthrough in its own right."

"The study of molecular machines, the dynamics of their moving parts and their translocation on molecular tracks is of great interest to nanotechnologists at the CNSI," said Weiss, the leader of the UCLA team. "Beyond furthering the understanding of transcription regulation, the novel methods and findings of this work will aid future studies of other molecular machines involved in cell replication, transcription and protein synthesis."

This work was funded by the National Institutes of Health, the U.S. Department of Energy and Howard Hughes Medical Institute.