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Crystal Structure Reveals New Details of Nonstandard RNA Transcription

“In the classical view of X-ray crystallography, you would think that the enzyme — RNA polymerase — would be inactivated and we couldn’t capture a biochemical process in action in a crystallized state,” said Katsuhiko S. Murakami, professor of biochemistry and molecular biology at Penn State and an author of the paper. “But in some systems, including ours, the RNA polymerase is still alive, so we can monitor the structures while they are in the process of making RNA.”

Reiterative transcription was discovered by Penn State alumnus and Nobel Laureate in chemistry Paul Berg, the Robert W. and Vivian K. Cahill Professor of Cancer Research, Emeritus, at Stanford University, in the early 1960s. Although it could appear to be a simple error in accurately transcribing the DNA sequence into RNA — reiterative transcription occurs when the strand of RNA slips relative to the strand of DNA inside the polymerase enzyme — it has function in the cell. Reiterative transcription plays a key role in controlling gene expression for many genes, but despite this important role, its mechanism has remained a black box.

“Our work,” said Vadim Molodtsov, a research associate at Penn State and an author of the paper. “By capturing the crystal structure of RNA polymerase during reiterative transcription, we were able to identify a new pathway used by RNA to exit the enzyme. Instead of leaving through the door, it sneaks out the window.”

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